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From: Norman M. <mor...@cs...> - 2007-09-26 14:44:39
|
Dear All, FYI! All the best, Norman -------- Original Message -------- Subject: [Msi-workgroups-board] MSI papers Date: Wed, 26 Sep 2007 10:31:40 +0100 From: Roy <Roy...@ma...> Reply-To: Roy...@ma... To: msi...@li... Dear All, You'll be please to hear that these are now out in Vol3(3) and available online. Details pasted below. Please let your co-authors know. Best wishes, Roy Special issue papers on Metabolomics Standards Initiative Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L.W., Goodacre, R., Hardy, N.W., Taylor, C., Fostel, J., Kristal, B. Kaddurah-Daouk, R., Mendes, P., van Ommen, B., Lindon, J.C. & Sansone, S.-A. (2007) The metabolomics standards initiative (MSI). /Metabolomics/ *3*, 175-178. Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H., Schuppe-Koistinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P., Rubtsov, D.V. & Robertson, D. (2007) Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments. /Metabolomics/ *3*, 179-188. van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T., Portais. J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M., Fostel, J. & Sauer, U. (2007) Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. /Metabolomics/ *3*, 189-194. Fiehn, O., Sumner, L.W., Rhee, S.Y., Ward, J., Dickerson, J., Lange, B.M., Lane, G., Roessner, U., Last, R. & Nikolau1, B. (2007) Minimum reporting standards for plant biology context information in metabolomic studies. /Metabolomics/ *3*, 195-201. Morrison, N., Bearden, D., Bundy, J.G., Collette, T., Currie, F., Davey, M.P., Haigh, N.S., Hancock, D., Jones, O.A.H., Rochfort, S., Sansone, S.-A., Štys, D., Teng, Q., Field, D. & Viant, M.R. (2007) Standard reporting requirements for biological samples in metabolomics experiments: environmental context. /Metabolomics/ *3*, 203-210. Sumner, L.W., Amberg, A., Barrett, D., Beger, R., Beale, M.H., Daykin, C., Fan, T.W.-M., Fiehn, O., Goodacre, R., Griffin, J.L., Hardy, N., Higashi, R., Kopka, J., Lindon, J.C., Lane, A.N., Marriott, P., Nicholls, A.W., Reily, M.D. & Viant, M. (2007) Proposed minimum reporting standards for chemical analysis. /Metabolomics/ *3*, 211-221. Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., Günther, U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting requirements for the description of NMR-based metabolomics experiments. /Metabolomics/ *3*, 223-229. Goodacre, R., Broadhurst, D., Smilde, A., Kristal, B.S., Baker, J.D., Beger, R., Bessant, C., Connor, S., Capuani, G., Craig, A., Ebbels, T., Kell, D.B., Manetti, C., Newton, J., Paternostro, G., Somorjai, R., Sjöström, M., Trygg, J. & Wulfert, F. (2007) Proposed minimum reporting standards for data analysis in metabolomics. /Metabolomics/ *3*, 231-241. Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of standard data exchange structures for metabolomics. /Metabolomics/ *3*, 243-248. Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H., Rocca-Serra, P., Rubtsov, D.V., Spasic, I., Soldatova, L., Taylor, C., Tseng, A., Viant, M.R. & The Ontology Working Group Members (2007) Metabolomics standards initiative - ontology working group - work in progress. /Metabolomics/ *3*, 249-256. PS: Metabolomics - the journal is now on ISI Submit your papers here: http://mebo.edmgr.com -- Prof. Roy Goodacre - Roy...@ma... School of Chemistry & Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK http://biospec.net Tel/Fax: +44 (0) 161 306 4480 / 4519 -- Dr Norman Morrison NEBC Omic Data Standards Coordinator (http://nebc.nox.ac.uk/) Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 |
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From: Oliver J. <oa...@mo...> - 2007-06-25 10:37:04
|
Dear Norman, Thanks for the mail. I've had a read through. It all looks good to me and my affiliation details etc are all fine. Thanks to everybody for their hard work on this. Best regards Oli PS: Congratulations Norman Norman Morrison wrote: >Dear All, > >The paper has reached the final proof stage. Many thanks to Mark for >getting it to this stage as I have been on annual leave for the past 3 >weeks (off getting married!). > >Finally, please can you check your affiliations. If I hear nothing from >you by Wednesday I will assume all is well and sign off. > >All the best, >Norman > >-------- Original Message -------- >Subject: Urgent proofs for your article in METABOLOMICS ( 67 ) >Date: Sat, 23 Jun 2007 12:33:10 +0530 >From: <Spr...@sp...> >To: <nor...@ma...> > > > >Article Title: STANDARD REPORTING REQUIREMENTS FOR BIOLOGICAL SAM >DOI: 10.1007/s11306-007-0067-1 >Editorial manuscript number: MEBO86.1 > >Dear Author, > >A PDF (portable document format) file of the page proofs of your article to appear in Metabolomics is available at > >https://www.e-proof.sps.co.in/springer-ny/ja.asp?rfp=iggfeison > >In order to minimize production time, these proofs are being sent to you directly from the compositor. > >Please read these page proofs carefully and return your corrections via email or fax. If you fax, please indicate in blue or black ink all corrections required for technical accuracy. Please do not make changes that involve only matters of style. We have generally introduced revisions that follow the journal's style. Substantial changes in content, e.g., new results, corrected values, title and authorship are not allowed without the approval of the journal's editor. In such a case, please contact the Editorial Office and return his/her consent together with the proof. > >Please return the marked proofs to us within 48 hours of receipt of this email so that publication may proceed on schedule. Let me know immediately if you anticipate any delay. If you are faxing the proofs please fax +1 347 649 2158 (US) or +44 207 806 8278 (UK) or +91 44 4208 9499 (India) or e-mail (spr...@sp...). > > >Thank you very much. We hope you are pleased with the publication. > >Sincerely yours, > > >Springer Correction Team > >No. 6&7, 5th Street, Radhakrishnan Salai >Mylapore, Chennai, Tamilnadu >India, Pincode 600 004 >e-mail: spr...@sp... >Fax: +1 347 649 2158 (US) or +44 207 806 8278 (UK) or +91 44 4208 9499 (India) > >Please note: > >Online Publication > >Your article will be published Online First. This is the official publication citable with the DOI. Further changes after this proof stage, therefore, are not possible. > >If you would like to know when your article has been published online, take advantage of our free alert service. For registration and further information go to: http://www.springerlink.com/ > >Ordering Reprints: To order reprints online, please go to: http://www.sheridan.com/springer/eoc > >If you prefer to fax the reprint order form you will also be able to download a form to use at that URL. All reprint order queries should be addressed to the contact information on the form. If your article contains color illustrations, please indicate on your reprint order form if you would like those illustrations in color in the reprints. In this case, please be sure to place your order within 14 days of receipt of proofs, as reprints with color are not available after the article has been published. > >Springer Open Choice > >Springer now offers authors the option, for a one-time fee, of making the published version of their articles available to all readers free of charge from SpringerLink. Springer Open Choice (http://www.springer.com/openchoice) is the program that provides this service. > >If you would like to order Open Choice for your article, please follow the link below to an order form for your article. > >http://www.springer.com/orderopenchoice?DOI=10.1007/s11306-007-0067-1&JID=11306&AT=%20STANDARD%20REPORTING%20REQUIREMENTS%20FOR%20BIOLOGICAL%20SAM > >Article Title: STANDARD REPORTING REQUIREMENTS FOR BIOLOGICAL SAM >Article DOI: 10.1007/s11306-007-0067-1 >Journal title: METABOLOMICS > >If for some reason you experience difficulties with this link, you can also go to an online order form at > >http://www.springer.com/east/home/open+choice/order+new?SGWID=5-40571-0-0-0 > >and enter the Article DOI for this article. > >If you are still having difficulties, please call us at >in the Americas: +1-800-SPRINGER (Journals Customer Service, USA) >in the rest of the world: +49-6221-345-4303 (Customer Service Journals, Germany) > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > > > |
|
From: Norman M. <mor...@cs...> - 2007-06-25 09:51:20
|
Dear All, The paper has reached the final proof stage. Many thanks to Mark for getting it to this stage as I have been on annual leave for the past 3 weeks (off getting married!). Finally, please can you check your affiliations. If I hear nothing from you by Wednesday I will assume all is well and sign off. All the best, Norman -------- Original Message -------- Subject: Urgent proofs for your article in METABOLOMICS ( 67 ) Date: Sat, 23 Jun 2007 12:33:10 +0530 From: <Spr...@sp...> To: <nor...@ma...> Article Title: STANDARD REPORTING REQUIREMENTS FOR BIOLOGICAL SAM DOI: 10.1007/s11306-007-0067-1 Editorial manuscript number: MEBO86.1 Dear Author, A PDF (portable document format) file of the page proofs of your article to appear in Metabolomics is available at https://www.e-proof.sps.co.in/springer-ny/ja.asp?rfp=iggfeison In order to minimize production time, these proofs are being sent to you directly from the compositor. Please read these page proofs carefully and return your corrections via email or fax. If you fax, please indicate in blue or black ink all corrections required for technical accuracy. Please do not make changes that involve only matters of style. We have generally introduced revisions that follow the journal's style. Substantial changes in content, e.g., new results, corrected values, title and authorship are not allowed without the approval of the journal's editor. In such a case, please contact the Editorial Office and return his/her consent together with the proof. Please return the marked proofs to us within 48 hours of receipt of this email so that publication may proceed on schedule. Let me know immediately if you anticipate any delay. If you are faxing the proofs please fax +1 347 649 2158 (US) or +44 207 806 8278 (UK) or +91 44 4208 9499 (India) or e-mail (spr...@sp...). Thank you very much. We hope you are pleased with the publication. Sincerely yours, Springer Correction Team No. 6&7, 5th Street, Radhakrishnan Salai Mylapore, Chennai, Tamilnadu India, Pincode 600 004 e-mail: spr...@sp... Fax: +1 347 649 2158 (US) or +44 207 806 8278 (UK) or +91 44 4208 9499 (India) Please note: Online Publication Your article will be published Online First. This is the official publication citable with the DOI. Further changes after this proof stage, therefore, are not possible. If you would like to know when your article has been published online, take advantage of our free alert service. For registration and further information go to: http://www.springerlink.com/ Ordering Reprints: To order reprints online, please go to: http://www.sheridan.com/springer/eoc If you prefer to fax the reprint order form you will also be able to download a form to use at that URL. All reprint order queries should be addressed to the contact information on the form. If your article contains color illustrations, please indicate on your reprint order form if you would like those illustrations in color in the reprints. In this case, please be sure to place your order within 14 days of receipt of proofs, as reprints with color are not available after the article has been published. Springer Open Choice Springer now offers authors the option, for a one-time fee, of making the published version of their articles available to all readers free of charge from SpringerLink. Springer Open Choice (http://www.springer.com/openchoice) is the program that provides this service. If you would like to order Open Choice for your article, please follow the link below to an order form for your article. http://www.springer.com/orderopenchoice?DOI=10.1007/s11306-007-0067-1&JID=11306&AT=%20STANDARD%20REPORTING%20REQUIREMENTS%20FOR%20BIOLOGICAL%20SAM Article Title: STANDARD REPORTING REQUIREMENTS FOR BIOLOGICAL SAM Article DOI: 10.1007/s11306-007-0067-1 Journal title: METABOLOMICS If for some reason you experience difficulties with this link, you can also go to an online order form at http://www.springer.com/east/home/open+choice/order+new?SGWID=5-40571-0-0-0 and enter the Article DOI for this article. If you are still having difficulties, please call us at in the Americas: +1-800-SPRINGER (Journals Customer Service, USA) in the rest of the world: +49-6221-345-4303 (Customer Service Journals, Germany) |
|
From: Dawn F. <df...@ce...> - 2007-05-18 19:22:33
|
Hi Norman,=20
great to see progress on this
UML =3D FuGE? Surely that must be a top-level MSI activity?=20=20
Feel free to develop an XML schema and view it in GenCat! :-) Would be a d=
oddle to set up (the webforms, I mean). I'd be happy to help.
It should be quite easy to do from the checklist, the bigger issue being th=
e UML...
Dawn
>>> Norman Morrison <mor...@cs...> 5/18/07 17:28 >>>
Dear All
Please find below the reviewers' comments to our ECWSG-MSI manuscript=20
submitted to Metabolomics.
The reviews have been quite favourable except for a couple of points=20
that need to be addressed from Reviewer No.1.
In brief these include the following suggestions:
1) a schema should be provided as well as a UML representation to assist=20
potential users and developers to understand and evaluate the proposed=20
standard...
2) provision of a mechanism for providing feedback on the proposed=20
standards that does NOT involve joining a mailing list
It is my understanding that most of the manuscripts have received=20
similar suggestions.
I think the second point is fairly easily addressed as one CAN send=20
emails to the list without signing up, it just requires moderator=20
approval (to avoid spamming the rest of you). Currently I am moderating=20
the but I can add anyone else that particularly enjoys moderating=20
mailing lists :-) Susanna has also suggested a mechanism for dealing=20
with this to the MSI board. If I've understood Susanna's suggestion=20
correctly, it is to set up a mail 'alias ' where comments are forwarded=20
on to a set of lists or individuals where they can be dealt with=20
appropriately. Does anyone else have any suggestions?
The first point is slightly more difficult to address and I think will=20
require a concerted response not only from our group, but from the=20
biological context working groups as a whole. The generation of=20
sub-group level schemas and UML representations is likely to be quite=20
redundant, open to misinterpretation if not considered in the wider=20
context and should really be approached from a cross working group=20
perspective. Does anyone else have any comments?**
**Chris Taylor and Nigel Hardy have already addressed these points quite=20
well to the MSI Board. I will forward their suggestions for your=20
consideration in a separate mail.
All the best,
Norman
--------------------
View Letter
Date: May 17, 2007
To: "Norman Morrison" mor...@cs...=20
From: "Metabolomics" roy...@ma...=20
Subject: Decision on your Manuscript #MEBO86
Dear Norman,
We have received the reports from our advisors on your manuscript,=20
"Standard Reporting Requirements for Biological Samples in Metabolomics=20
Experiments: Environmental Context.", which you submitted to Metabolomics.
Based on the advice received, I feel your manuscript could be accepted=20
for publication should you be prepared to incorporate minor revisions.=20=
=20
When preparing your revised manuscript, you are asked to carefully=20
consider the reviewer comments which are attached, and submit a list of=20
responses to the comments. Your list of responses should be uploaded as=20
a file in addition to your revised manuscript.
We look forward to receiving your revised manuscript.
Best regards,
Royston Goodacre, PhD
Editor-in-Chief
Metabolomics
COMMENTS FOR THE AUTHOR:
REVIEWER 1: MEBO86
The manuscript by Morrison and colleagues presents a proposed "Standard=20
Reporting Requirements for Biological Samples in Metabolomics=20
Experiments: Environmental Context" as part of a larger effort to=20
establish standards for metabolomics experiments.
The manuscript describes the way in which the standard was developed and=20
lays out the intellectual frame work upon which it is based. Relative to=20
other proposed standards in this issue, what is presented here is=20
relatively underdeveloped. However, this is an important addition to the=20
body of standards and should be included.
In general, the manuscript does a reasonable job of presenting the=20
proposed standard and opens solicitation for feedback from the=20
community. Unfortunately, the manuscript does not include a schema and=20
one should be provided as well as a UML representation to assist=20
potential users and developers to understand and evaluate the proposed=20
standard. The manuscript also lacks a mechanism of providing feedback on=20
the proposed standards short of joining a mailing list, something that=20
may prevent many from contributing comments. This should be addressed=20
prior to publication.
REVIEWER 2: Comments on Manuscript MEBO86 entitled =AB Standard reporting=
=20
requirements for biological samples in metabolomics experiments :=20
environmental context =BB
The manuscript by Morrison. et al. entitled " Standard reporting=20
requirements for biological samples in metabolomics experiments :=20
environmental context " details standard reporting requirements for=20
describing biological samples and their environmental factors in the=20
context of metabolomic experiments.
I thought the paper was very interesting scientifically by providing=20
compelling evidence of needs for rigorous and flexible experimental=20
designs aiming at capturing the maximum of the environmental=20
contribution to metabolic profiles in a structured and comprehensive=20
form. Moreover, the paper highlights the position of this effort of=20
standardisation in the context of all the omics techniques, including=20
genomics, proteomics and previous efforts on metabolomics and in=20
collaboration with other recognized initiatives. The description of the=20
reporting requirements is made clear and exhaustive whilst remaining an=20
open source to add and define further the actual descriptors.
I recommend the paper for publication.
-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/=20
_______________________________________________
Msi-workgroups-env-bio-metadata mailing list
Msi...@li...=20
https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata
--=20
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.
|
|
From: Susanna <sa...@eb...> - 2007-05-18 17:14:49
|
Hi All, Norman Morrison wrote: >Dear All > >Please find below the reviewers' comments to our ECWSG-MSI manuscript >submitted to Metabolomics. > >The reviews have been quite favourable except for a couple of points >that need to be addressed from Reviewer No.1. > >In brief these include the following suggestions: >1) a schema should be provided as well as a UML representation to assist >potential users and developers to understand and evaluate the proposed >standard... >2) provision of a mechanism for providing feedback on the proposed >standards that does NOT involve joining a mailing list > >It is my understanding that most of the manuscripts have received >similar suggestions. > >I think the second point is fairly easily addressed as one CAN send >emails to the list without signing up, it just requires moderator >approval (to avoid spamming the rest of you). Currently I am moderating >the but I can add anyone else that particularly enjoys moderating >mailing lists :-) Susanna has also suggested a mechanism for dealing >with this to the MSI board. If I've understood Susanna's suggestion >correctly, it is to set up a mail 'alias ' where comments are forwarded >on to a set of lists or individuals where they can be dealt with >appropriately. Does anyone else have any suggestions? > It was our reviewer who suggested this, as alias. I have proposed to the board to have one only for the WGs. We do not what to mantain lots of lists... > >The first point is slightly more difficult to address and I think will >require a concerted response not only from our group, but from the >biological context working groups as a whole. The generation of >sub-group level schemas and UML representations is likely to be quite >redundant, open to misinterpretation if not considered in the wider >context and should really be approached from a cross working group >perspective. Does anyone else have any comments?* > > >**Chris Taylor and Nigel Hardy have already addressed these points quite >well to the MSI Board. I will forward their suggestions for your >consideration in a separate mail. > Indeed. This is what the Format/Exchange WG is there for!!!! Thanks Norman!! Susanna > >All the best, >Norman > >-------------------- > > >View Letter >Date: May 17, 2007 >To: "Norman Morrison" mor...@cs... >From: "Metabolomics" roy...@ma... >Subject: Decision on your Manuscript #MEBO86 > >Dear Norman, > >We have received the reports from our advisors on your manuscript, >"Standard Reporting Requirements for Biological Samples in Metabolomics >Experiments: Environmental Context.", which you submitted to Metabolomics. > >Based on the advice received, I feel your manuscript could be accepted >for publication should you be prepared to incorporate minor revisions. >When preparing your revised manuscript, you are asked to carefully >consider the reviewer comments which are attached, and submit a list of >responses to the comments. Your list of responses should be uploaded as >a file in addition to your revised manuscript. > >We look forward to receiving your revised manuscript. > >Best regards, > > Royston Goodacre, PhD > Editor-in-Chief > Metabolomics > > >COMMENTS FOR THE AUTHOR: > >REVIEWER 1: MEBO86 > >The manuscript by Morrison and colleagues presents a proposed "Standard >Reporting Requirements for Biological Samples in Metabolomics >Experiments: Environmental Context" as part of a larger effort to >establish standards for metabolomics experiments. > >The manuscript describes the way in which the standard was developed and >lays out the intellectual frame work upon which it is based. Relative to >other proposed standards in this issue, what is presented here is >relatively underdeveloped. However, this is an important addition to the >body of standards and should be included. > >In general, the manuscript does a reasonable job of presenting the >proposed standard and opens solicitation for feedback from the >community. Unfortunately, the manuscript does not include a schema and >one should be provided as well as a UML representation to assist >potential users and developers to understand and evaluate the proposed >standard. The manuscript also lacks a mechanism of providing feedback on >the proposed standards short of joining a mailing list, something that >may prevent many from contributing comments. This should be addressed >prior to publication. > > >REVIEWER 2: Comments on Manuscript MEBO86 entitled « Standard reporting >requirements for biological samples in metabolomics experiments : >environmental context » > >The manuscript by Morrison. et al. entitled " Standard reporting >requirements for biological samples in metabolomics experiments : >environmental context " details standard reporting requirements for >describing biological samples and their environmental factors in the >context of metabolomic experiments. > >I thought the paper was very interesting scientifically by providing >compelling evidence of needs for rigorous and flexible experimental >designs aiming at capturing the maximum of the environmental >contribution to metabolic profiles in a structured and comprehensive >form. Moreover, the paper highlights the position of this effort of >standardisation in the context of all the omics techniques, including >genomics, proteomics and previous efforts on metabolomics and in >collaboration with other recognized initiatives. The description of the >reporting requirements is made clear and exhaustive whilst remaining an >open source to add and define further the actual descriptors. > >I recommend the paper for publication. > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > > -- Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: sa...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK room: A229 |
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From: Norman M. <mor...@cs...> - 2007-05-18 16:35:28
|
Dear ECWSG members, Please find below Nigel and Chris' responses to the Chemical analysis working group manuscript. FYI, the reviewers comments were essentially the same as for our manuscript. Kind regards, Norman --- Nigel Hardy's response to reviewers' comments to Chemical analysis working group manuscript --- That's our job! :-) More seriously, this is the larger job which we all need to do in the context of the other WGs and strategic decisions about top level structures for the whole initiative. I suggest that the comment reflects a failure to put the paper in the wider MSI context or the reviewer's failure to understand this. Perhaps a stronger pointer to the overview document would help? At a lower level, we have recently attempted a first modelling and schema coding exercise for xC-MS and have a few detailed questions and comments on the Chem Analysis document. I have not yet found time to formulate these but will push to do that so that, if appropriate, they could be incorporated into the new version. Nigel --- Chirs Taylor's response to reviewers' comments to Chemical analysis working group manuscript --- Hi all. I have to say that while some sort of figure might assist the most chronically visual of thinkers it is essentially redundant. In _all_ other (~near) equivalent documents the only concession to brevity/clarity is a bulleted list of points, indented as necessary to give some structure for the eye. This of course mandates a fuller glossary, ideally with examples, to avoid misinterpretation. But fundamentally, to stray too close to producing a data model (a job being done elsewhere) and worse, one that (by its very nature, were this request to be followed) only supports the precise spec being described, hindering interoperability, is both redundant and confusing. I suggest that in _all_ cases this request is resisted. Bespoke data models will defeat not just attempts to provide a set of efficient formats for MSI but far more seriously, attempts to provide cross-domain models that assist us as we move towards fully-fledged (i.e meaningfully integrated) systems biology. As I say a graphical representation cannot hurt, per se, if it cannot be interpreted as a nascent data model (although I think it adds nothing as it would just be a bulleted list, but with boxes round the first order bullets and their immediate children and lines between), but to stray too far into building bespoke models is a waste of time (and potentially damaging to the coordination and apportioning of roles across MSI and more broadly). So my (ineligible, admittedly) vote: Rebut! Points for the rebuttal (and _maybe_ for the ms itself) could include: (1) More reference to the context within MSI (model coming from elsewhere, along with CV terms) (2) More reference to the broader context -- mention FuGE which will ultimately cure all ills, OBI even (and one more below, maybe) and that it is inappropriate to 'bundle' a bespoke format with the guidelines (which, for example, may be supported by vendors in their software, by databases of various kinds, by many other formats including of course those from within MSI and partners -- all of which would be hindered by even giving the appearance of only 'recognising' the required data as 'standard' if it is in the para-data model suggested by the review). (3) (trivial) People _can_ email the list direct without signing up -- this occurs with the PSI lists (exactly the same mechanism) all the time and all it takes is moderator approval to have them passed along to the recipients -- a single mail account is not a good option as one person has to field them all (and probably pass them along to a list anyway) and there is no automatic archive that can be searched/browsed (so really, a non-point but perhaps a little more explanation could help). (4) Do any of the guidelines people specifically fancy giving some thought to MIBBI's coming intergration project; i.e. the option to combine (after maturation) MSI's guidelines with the many many (many) other groups now involved in similar projects? Have a browse around mibbi.sf.net to get a flavour (the paper recently accepted by Nature Biotech is there along with other goodies including a first pass cross analysis of guidelines to highlight overlaps that suggest common models). FYI for the more clinically-minded amongst you there's a parallel international 'meta-project' starting up now for clinical guidelines too (with which MIBBI is to soon become affiliated -- linked from the news page on MIBBI -- it's called EQUATOR). Anyway I think I made my points (at some length -- sorry). Cheers, Chris in curmudgeonly mood. |
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From: Norman M. <mor...@cs...> - 2007-05-18 16:28:21
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Dear All
Please find below the reviewers' comments to our ECWSG-MSI manuscript
submitted to Metabolomics.
The reviews have been quite favourable except for a couple of points
that need to be addressed from Reviewer No.1.
In brief these include the following suggestions:
1) a schema should be provided as well as a UML representation to assist
potential users and developers to understand and evaluate the proposed
standard...
2) provision of a mechanism for providing feedback on the proposed
standards that does NOT involve joining a mailing list
It is my understanding that most of the manuscripts have received
similar suggestions.
I think the second point is fairly easily addressed as one CAN send
emails to the list without signing up, it just requires moderator
approval (to avoid spamming the rest of you). Currently I am moderating
the but I can add anyone else that particularly enjoys moderating
mailing lists :-) Susanna has also suggested a mechanism for dealing
with this to the MSI board. If I've understood Susanna's suggestion
correctly, it is to set up a mail 'alias ' where comments are forwarded
on to a set of lists or individuals where they can be dealt with
appropriately. Does anyone else have any suggestions?
The first point is slightly more difficult to address and I think will
require a concerted response not only from our group, but from the
biological context working groups as a whole. The generation of
sub-group level schemas and UML representations is likely to be quite
redundant, open to misinterpretation if not considered in the wider
context and should really be approached from a cross working group
perspective. Does anyone else have any comments?**
**Chris Taylor and Nigel Hardy have already addressed these points quite
well to the MSI Board. I will forward their suggestions for your
consideration in a separate mail.
All the best,
Norman
--------------------
View Letter
Date: May 17, 2007
To: "Norman Morrison" mor...@cs...
From: "Metabolomics" roy...@ma...
Subject: Decision on your Manuscript #MEBO86
Dear Norman,
We have received the reports from our advisors on your manuscript,
"Standard Reporting Requirements for Biological Samples in Metabolomics
Experiments: Environmental Context.", which you submitted to Metabolomics.
Based on the advice received, I feel your manuscript could be accepted
for publication should you be prepared to incorporate minor revisions.
When preparing your revised manuscript, you are asked to carefully
consider the reviewer comments which are attached, and submit a list of
responses to the comments. Your list of responses should be uploaded as
a file in addition to your revised manuscript.
We look forward to receiving your revised manuscript.
Best regards,
Royston Goodacre, PhD
Editor-in-Chief
Metabolomics
COMMENTS FOR THE AUTHOR:
REVIEWER 1: MEBO86
The manuscript by Morrison and colleagues presents a proposed "Standard
Reporting Requirements for Biological Samples in Metabolomics
Experiments: Environmental Context" as part of a larger effort to
establish standards for metabolomics experiments.
The manuscript describes the way in which the standard was developed and
lays out the intellectual frame work upon which it is based. Relative to
other proposed standards in this issue, what is presented here is
relatively underdeveloped. However, this is an important addition to the
body of standards and should be included.
In general, the manuscript does a reasonable job of presenting the
proposed standard and opens solicitation for feedback from the
community. Unfortunately, the manuscript does not include a schema and
one should be provided as well as a UML representation to assist
potential users and developers to understand and evaluate the proposed
standard. The manuscript also lacks a mechanism of providing feedback on
the proposed standards short of joining a mailing list, something that
may prevent many from contributing comments. This should be addressed
prior to publication.
REVIEWER 2: Comments on Manuscript MEBO86 entitled « Standard reporting
requirements for biological samples in metabolomics experiments :
environmental context »
The manuscript by Morrison. et al. entitled " Standard reporting
requirements for biological samples in metabolomics experiments :
environmental context " details standard reporting requirements for
describing biological samples and their environmental factors in the
context of metabolomic experiments.
I thought the paper was very interesting scientifically by providing
compelling evidence of needs for rigorous and flexible experimental
designs aiming at capturing the maximum of the environmental
contribution to metabolic profiles in a structured and comprehensive
form. Moreover, the paper highlights the position of this effort of
standardisation in the context of all the omics techniques, including
genomics, proteomics and previous efforts on metabolomics and in
collaboration with other recognized initiatives. The description of the
reporting requirements is made clear and exhaustive whilst remaining an
open source to add and define further the actual descriptors.
I recommend the paper for publication.
|
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From: Norman M. <mor...@cs...> - 2007-03-21 08:21:51
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I should probably clarify that 'credit' at this stage will be a name for the provider of the term and their affiliation in the ontology. Unless a significant contribution has been made, it is unlikely that this will mean 'towards publication'. I just didn't want anyone thinking I was hoovering up all the terms and passing them off as my own work :-) I should also add that there is a logistical reason for providing the terms through a community representative. Although OBI is already a very large effort, it is still in a formative stage of development. At the moment it would be unrealistic to have too many individuals representing each community. Norman Morrison wrote: > Dear All, > > I'm afraid I still have no news re the paper. > > However, I do have a favour to ask! > > I am in the process of collecting biomaterial terms for the Ontology > of Biomedical Investigations (OBI), specifically from the 'Env' > community. > > If you have 5 mins, could I ask you to put together a short list of > the top 5 (more if you like) terms you would use to describe > biomaterials you work with day to day in your investigations. > > NB - Please could you also provide a concise definition for these > terms, otherwise they will be very much open to interpretation. > > For example: > > Term: Soil > Definition: Mixture of minerals and organic matter. > > What is a biomaterial? > A biomaterial entity is an object of biological origin. In simple > terms, it can be any type of 'sample' in any form that is used in a > biological investigation. > > What's in it for you? > Anyone providing terms for use in the ontology will receive due credit > and the terms that are provided will be tagged as affiliated with this > effort. Plus, when you come to use the ontology the terms will be > there already! > > Looking forward to your response. > > All the best, > Norman > > |
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From: Norman M. <mor...@cs...> - 2007-03-20 21:46:13
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Dear All, I'm afraid I still have no news re the paper. However, I do have a favour to ask! I am in the process of collecting biomaterial terms for the Ontology of Biomedical Investigations (OBI), specifically from the 'Env' community. If you have 5 mins, could I ask you to put together a short list of the top 5 (more if you like) terms you would use to describe biomaterials you work with day to day in your investigations. NB - Please could you also provide a concise definition for these terms, otherwise they will be very much open to interpretation. For example: Term: Soil Definition: Mixture of minerals and organic matter. What is a biomaterial? A biomaterial entity is an object of biological origin. In simple terms, it can be any type of 'sample' in any form that is used in a biological investigation. What's in it for you? Anyone providing terms for use in the ontology will receive due credit and the terms that are provided will be tagged as affiliated with this effort. Plus, when you come to use the ontology the terms will be there already! Looking forward to your response. All the best, Norman |
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From: Norman M. <mor...@cs...> - 2007-02-23 10:28:31
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Dear All, A couple of you have contacted me asking if there had been any news yet about the MSI paper. So, I mailed Roy and received this from him today. Lets just hope no news is good news! All the best, Norman >From Roy Goodacre: > Dear Norman > > No news yet - will let all of you know as soon as I have any. > > Best wishes, Roy |
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From: Norman M. <mor...@cs...> - 2007-01-05 13:35:53
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Ooops, my apologies I meant to attach this earlier :-) Oliver Jones wrote: > Dear Norman, > > It all looks good to me. > > Cheers > > Oli > > Matthew Davey wrote: > > >> Thanks Norman, >> >> All of the linked petraea files are fine. >> >> Also, would you mind emailing out the final submitted document? >> >> Many thanks, >> >> Matt >> >> >> -----Original Message----- >> From: msi...@li... >> [mailto:msi...@li...] On >> Behalf Of Norman Morrison >> Sent: 05 January 2007 12:49 >> To: msi...@li... >> Subject: [Msi-workgroups-env-bio-metadata] Supplementary Information >> >> Dear All, >> >> I've constructed a rudimentary web page that details the supplementary >> information included in the paper. Please can those of you that provided >> examples check that your files are referenced correctly and that you are >> happy with them. There are no links from the other MSI pages yet, so you >> can only navigate to it directly. >> >> http://msi-workgroups.sourceforge.net/bio-metadata/reporting/env/ >> >> Comments/suggestions? >> >> Cheers, >> Norman >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Msi-workgroups-env-bio-metadata mailing list >> Msi...@li... >> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Msi-workgroups-env-bio-metadata mailing list >> Msi...@li... >> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >> >> >> >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Msi-workgroups-env-bio-metadata mailing list > Msi...@li... > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > -- Dr Norman Morrison NERC Omic Data Standards Coordinator Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 |
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From: Oliver J. <oa...@mo...> - 2007-01-05 13:29:23
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Dear Norman, It all looks good to me. Cheers Oli Matthew Davey wrote: >Thanks Norman, > >All of the linked petraea files are fine. > >Also, would you mind emailing out the final submitted document? > >Many thanks, > >Matt > > >-----Original Message----- >From: msi...@li... >[mailto:msi...@li...] On >Behalf Of Norman Morrison >Sent: 05 January 2007 12:49 >To: msi...@li... >Subject: [Msi-workgroups-env-bio-metadata] Supplementary Information > >Dear All, > >I've constructed a rudimentary web page that details the supplementary >information included in the paper. Please can those of you that provided >examples check that your files are referenced correctly and that you are >happy with them. There are no links from the other MSI pages yet, so you >can only navigate to it directly. > >http://msi-workgroups.sourceforge.net/bio-metadata/reporting/env/ > >Comments/suggestions? > >Cheers, >Norman > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > > > |
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From: Matthew D. <m....@sh...> - 2007-01-05 12:55:04
|
Thanks Norman, All of the linked petraea files are fine. Also, would you mind emailing out the final submitted document? Many thanks, Matt -----Original Message----- From: msi...@li... [mailto:msi...@li...] On Behalf Of Norman Morrison Sent: 05 January 2007 12:49 To: msi...@li... Subject: [Msi-workgroups-env-bio-metadata] Supplementary Information Dear All, I've constructed a rudimentary web page that details the supplementary information included in the paper. Please can those of you that provided examples check that your files are referenced correctly and that you are happy with them. There are no links from the other MSI pages yet, so you can only navigate to it directly. http://msi-workgroups.sourceforge.net/bio-metadata/reporting/env/ Comments/suggestions? Cheers, Norman ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Msi-workgroups-env-bio-metadata mailing list Msi...@li... https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata |
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From: Norman M. <mor...@cs...> - 2007-01-05 12:48:59
|
Dear All, I've constructed a rudimentary web page that details the supplementary information included in the paper. Please can those of you that provided examples check that your files are referenced correctly and that you are happy with them. There are no links from the other MSI pages yet, so you can only navigate to it directly. http://msi-workgroups.sourceforge.net/bio-metadata/reporting/env/ Comments/suggestions? Cheers, Norman |
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From: Norman M. <mor...@cs...> - 2007-01-05 12:43:42
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Dear All, The paper has been submitted! Thank you for all your hard work and continued involvement. I will keep you posted on it's progress. All the best, Norman |
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From: Mark V. <m....@bh...> - 2007-01-05 11:42:32
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Hi Norman - Not a huge issue. There will be a lot of fine tuning in the=20 future. I am happy to submit as is. Cheers Mark At 10:44 05/01/2007, Norman Morrison wrote: >Dear All, > >This is a very good point. However, taking the big picture view, I think >the requirements will continue to evolve and we clearly state this in >the paper. I'm about to submit and I think this issue will require >further discussion, so I suggest we leave the requirements as they stand >and address this point in our online version of the requirements in the >near future? > >All the best, >Norman > > >Oliver Jones wrote: > > Dear all, > > > > I think perhaps temperature could be moved to the 'other measured > > parameters' section along with pH and organic content but I don't > > think it makes a huge difference. > > > > Oli > > > > Jake Bundy wrote: > >> No major changes at this point (one or two things I would word > >> slightly differently is all). > >> > >> The sole scientific question/suggestion I have is that, under section > >> E3.1 (description of terrestrial environment), 'substrate > >> temperature' should /not /be a top-level category (maybe this is more > >> appropriate for sediment sampling? in which case it shouldn't be > >> generalized to all terrestrial environments). But if the majority > >> disagree I'm happy to concede this point. > >> > >> > >> jake > >> > >> > >> > >> > >> ------------------------------------------ > >> Dr Jake Bundy > >> > >> Biomolecular Medicine > >> Sir Alexander Fleming Building > >> Imperial College > >> London SW7 2AZ > >> > >> j....@im... <mailto:j....@im...> > >> > >> Tel. +44 (0)20 75943039 > >> Fax +44 (0)20 75943226 > >> > >> > >> > >> On 4 Jan 2007, at 15:20, Oliver Jones wrote: > >> > >>> Dear all, > >>> > >>> I've attached my comments on version 7 of the paper. I think it is > >>> pretty much there now and although Susanna made some interesting > >>> comments I think they are fairly minor and can be resolved by the > >>> editors or maybe even the reviewers. I don't have anything much > >>> extra to add at this stage except that I would be in favour of > >>> submitting the paper tomorrow as planned. Norman - do we need to > >>> suggest reviewers in the cover letter or will Metabolomics do that > >>> at their end? > >>> > >>> My first e-mail this morning may have sounded a little more grumpy > >>> then I intended, apologies if so. Please also find attached an > >>> updated user case and real world example. These are based on similar > >>> but separate metabolomics based studies to avoid it looking like the > >>> real world example was retroactively fitted to the standards. > >>> > >>> I hope this is all OK but if you have any comments please just let > >>> me know. > >>> > >>> Best regards > >>> > >>> Oli > >>> > >>> > >>> > >>> Susanna wrote: > >>>> Hi Norman, > >>>> > >>>> please see page 1-4-9-20 only for some suggestions. > >>>> <<Env Metab Rep Reqs_v7-SS.doc>> > >>>> > >>>> Btw, MIGS is in NBT: http://www.nature.com/nbt/consult/index.html > >>>> You have to update the ref ! > >>>> > >>>> Thanks, > >>>> Susanna > >>>> > >>>> > >>>> Norman Morrison wrote: > >>>>> Dear All, > >>>>> > >>>>> Thanks for the info Susanna. It's useful to know that we have an > >>>>> extension until Monday/Tuesday next week, but I think our paper is > >>>>> basically finished. Actually, I don't know about everyone else, > >>>>> but I would prefer to get this paper out of the way and sent off > >>>>> tomorrow and would prefer if we stuck to this deadline. > >>>>> > >>>>> I have received a few separately submitted comments on version 6 - > >>>>> so, I've collated these and created version 7. Just in case any of > >>>>> you have further comments you would like to add please make them > >>>>> on this version (it makes my job a bit easier). > >>>>> > >>>>> All the best, > >>>>> Norman > >>>>> > >>>>> > >>>>> > >>>>> Susanna wrote: > >>>>>> Hi Norman and All, > >>>>>> > >>>>>> great job! > >>>>>> I suggest not to worry on this too much, as the editors will make > >>>>>> such suggestions/changes. > >>>>>> > >>>>>> Quick note to say that have just called Roy, Chief Editor, and we > >>>>>> have still few more days (Monday/Tuesday next week would be fine)!! > >>>>>> We/Ontology WG will produce a final version today, so these extra > >>>>>> days are key for us. > >>>>>> > >>>>>> Happy New Year! > >>>>>> Susanna > >>>>>> > >>>>>> Norman Morrison wrote: > >>>>>>> Dear All, > >>>>>>> > >>>>>>> I agree that the use of different fonts is not ideal. > >>>>>>> > >>>>>>> So far the options seem to be: > >>>>>>> > >>>>>>> 1) Matt's suggestion that we don't give 'sub-heading' status to > >>>>>>> S1 =AD Description of the =85etc. and revert back to italics for > >>>>>>> optional items. > >>>>>>> 2) Oli's use of colour. I picked up an example copy of > >>>>>>> metabolomics at the metaboconf3 and it didn't have any colour in > >>>>>>> it. > >>>>>>> 3) Felicities use of asterisks'. > >>>>>>> > >>>>>>> I am happy to go with Matt's suggestion - alternatively we could > >>>>>>> leave it as it as and ask the formatting editor of the journal > >>>>>>> if they have any advice. I think at this stage it should still > >>>>>>> be clear to reviewers what we consider optional. > >>>>>>> > >>>>>>> Norman > >>>>>>> > >>>>>>> Matthew Davey wrote: > >>>>>>>> Dear all, > >>>>>>>> > >>>>>>>> I agree with Oli in that the times roman/arial fonts are > >>>>>>>> difficult to distinguish. > >>>>>>>> > >>>>>>>> I have lifted my comment from my previous edited document as > >>>>>>>> one solution: > >>>>>>>> > >>>>>>>> =91Still not sure about using different fonts to distinguish > >>>>>>>> recommended and optional information. Some websites offer html > >>>>>>>> download instead of pdf, in which case it will all be in the > >>>>>>>> same font. One option is to have the subheadings eg. S1 =AD > >>>>>>>> Description of the =85 as non-italics as they already standout > >>>>>>>> due to the S1 etc code at the start and then have the =91optional > >>>>>>>> information=92 bits in italics.=92 > >>>>>>>> > >>>>>>>> Cheers, > >>>>>>>> > >>>>>>>> Matt > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------ > >>>>>>>> > >>>>>>>> > >>>>>>>> *From:* > >>>>>>>> msi...@li... > >>>>>>>>=20 > [mailto:msi...@li...] > >>>>>>>> *On Behalf Of *Oliver Jones > >>>>>>>> *Sent:* 04 January 2007 10:17 > >>>>>>>> *To:* msi...@li... > >>>>>>>> *Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version > >>>>>>>> 6 - final comments by tomorrow please! > >>>>>>>> > >>>>>>>> Dear all, > >>>>>>>> > >>>>>>>> First off, a very happy new year to you all. I hope everybody > >>>>>>>> enjoyed the holidays? > >>>>>>>> > >>>>>>>> Right, now to business, swooping in at the very last minute as > >>>>>>>> usualy I have a few comments on different things. > >>>>>>>> > >>>>>>>> > >>>>>>>> *1) The paper* > >>>>>>>> > >>>>>>>> This looks excellent, thanks to everybody for the hard work. I > >>>>>>>> hope it is not too late but I'm made a few minor changes and > >>>>>>>> comments to version 6 (attached) which I think may be of > >>>>>>>> use/interest. In response to Normans question I think the > >>>>>>>> following 'optional' form should be left as it is. > >>>>>>>> > >>>>>>>> o Include details such as the type of housing, for example: > >>>>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. > >>>>>>>> > >>>>>>>> I also agree with Mark and Norman that the merging of > >>>>>>>> "description" and "means" is a good idea for now. > >>>>>>>> > >>>>>>>> My only big worry is the use of the aerial font for optional > >>>>>>>> only parameters. I am not sure it shows up that well and I > >>>>>>>> personally find it a bit confusing especially if I convert the > >>>>>>>> document to a pdf. Unfortunately, I am at a loss at what else > >>>>>>>> to suggest except maybe different colours. However, that would > >>>>>>>> probably be quite difficult so I think we may just have to go > >>>>>>>> with what we have. > >>>>>>>> > >>>>>>>> *2) Use case/real world examples/project description > >>>>>>>> > >>>>>>>> *There seems to be some confusion here. When I was formulating > >>>>>>>> and commenting on what I thought should be included in the > >>>>>>>> requirements I tried to draw on all my experience in > >>>>>>>> Environmental Science and metabolomics. Admittedly this may not > >>>>>>>> be as extensive as some of the people in the group but I still > >>>>>>>> did not draw exclusively from just the one project. To that end > >>>>>>>> the described in my user case/real word example/insert your > >>>>>>>> description here was not retrofitted to the standards but was > >>>>>>>> worked through from the beginning and it took a fair while to > >>>>>>>> do. I think this is what Dalibor was trying to do as well. > >>>>>>>> (Speaking of Dalibor's examples I spotted a small mistake on > >>>>>>>> page 5, under section P5 =AD Description of acclimation of > >>>>>>>> organism(s), in that it still refers to the worms from my > >>>>>>>> project. This will need to be changed I think. There are also > >>>>>>>> several references in the text but no reference list at the end > >>>>>>>> of the document). I think it is very useful to have both user > >>>>>>>> cases on the website so people cna see what are proposing that > >>>>>>>> they write. > >>>>>>>> > >>>>>>>> I do take Normans point about why user cases are useful though. > >>>>>>>> However, I send round something along those lines several weeks > >>>>>>>> ago that was reasonably comprehensive so perhaps we could just > >>>>>>>> use that??? However, if you want something more comprehensive I > >>>>>>>> am afraid you will have to give me a bit more time to prepare > >>>>>>>> it (like an afternoon). Either way please let me know ASAP. > >>>>>>>> > >>>>>>>> Cheers > >>>>>>>> > >>>>>>>> Oli > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Mark Viant wrote: > >>>>>>>> > >>>>>>>> Dear Norm et al > >>>>>>>> > >>>>>>>> I editted version 5, was about to send, and version 6 appeared! > >>>>>>>> So cut/paste my comments into latest version. All minor (except > >>>>>>>> you cut a reference). I am happy for this to be sent. Agree > >>>>>>>> that merging "description" and "means" is a good idea for now. > >>>>>>>> Mark > >>>>>>>> > >>>>>>>> > >>>>>>>> At 13:35 03/01/2007, Norman Morrison wrote: > >>>>>>>> > >>>>>>>> Dear All, > >>>>>>>> > >>>>>>>> Please find attached version 6(!) of the paper. I hoped to > >>>>>>>> circulate this yesterday but it took a bit longer than I had > >>>>>>>> hoped. I think I have now addressed all of the previous issues > >>>>>>>> and have commented the sections that I have changed. If you > >>>>>>>> feel I have missed anything or any of the issues have not been > >>>>>>>> adequately addressed please let me know :-) > >>>>>>>> > >>>>>>>> There was one issue that I think will require more thought. In > >>>>>>>> the process requirement groups there was a motion to merge > >>>>>>>> 'Description' and 'Means of' together. In my mind I believed > >>>>>>>> that processes should include a concise, 'free text' > >>>>>>>> /description/, detailing the specific process that has been > >>>>>>>> applied or taken place, and that one should also aim to provide > >>>>>>>> a term(s) for the /means/ used (preferably from an ontology or > >>>>>>>> CV) in the application of the process. However, 'means' seems > >>>>>>>> to be a bit of a vague term, in that the examples we ourselves > >>>>>>>> provide, include descriptive terms that mix /actions/ (netted, > >>>>>>>> electrically stunned, etc) and /things/ (dry ice, > >>>>>>>> formaldehyde). Given this ambiguity, I think it might be best > >>>>>>>> if we depricated 'means' for the paper, but I think it will be > >>>>>>>> worth revisiting in the next version of the requirements. > >>>>>>>> > >>>>>>>> At the moment, I have kept the examples in the following > >>>>>>>> 'optional' form (see the paper): > >>>>>>>> > >>>>>>>> o Include details such as the type of housing, for example: > >>>>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. > >>>>>>>> > >>>>>>>> ...or we could just get rid of them altogether. Thoughts? > >>>>>>>> > >>>>>>>> Hopefully there are not too many more changes to make at this > >>>>>>>> late stage, but I welcome your comments. Please can you get > >>>>>>>> them back to me by *12pm (GMT) tomorrow* at the latest, so that > >>>>>>>> I can incorporate them into the final version for submission. > >>>>>>>> > >>>>>>>> Thanks, > >>>>>>>> Norman > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------- > >>>>>>>> > >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT > >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance > >>>>>>>> to share your > >>>>>>>> opinions on IT & business topics through brief surveys - and > >>>>>>>> earn cash > >>>>>>>>=20 >= http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DDE= VDEV_______________________________________________=20 > > >>>>>>>>=20 >= <http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV_______________________________________________>=20 > > >>>>>>>> > >>>>>>>> Msi-workgroups-env-bio-metadata mailing list > >>>>>>>> Msi...@li... > >>>>>>>> <mailto:Msi...@li...> > >>>>>>>>=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Dr. Mark Viant > >>>>>>>> NERC Advanced Fellow in Metabolomics > >>>>>>>> School of Biosciences > >>>>>>>> The University of Birmingham > >>>>>>>> Birmingham, B15 2TT, U.K. > >>>>>>>> Phone +44-(0)121-414-2219 > >>>>>>>> FAX +44-(0)121-414-5925 > >>>>>>>> http://www.biosciences.bham.ac.uk/labs/viant/ > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------ > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------- > >>>>>>>> > >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT > >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance > >>>>>>>> to share your > >>>>>>>> opinions on IT & business topics through brief surveys - and > >>>>>>>> earn cash > >>>>>>>>=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV > >>>>>>>>=20 >= <http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------ > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Msi-workgroups-env-bio-metadata mailing list > >>>>>>>> Msi...@li... > >>>>>>>> <mailto:Msi...@li...> > >>>>>>>>=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------ > >>>>>>>> > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------- > >>>>>>>> > >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT > >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance > >>>>>>>> to share your > >>>>>>>> opinions on IT & business topics through brief surveys - and > >>>>>>>> earn cash > >>>>>>>>=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV > >>>>>>>> > >>>>>>>>=20 > ------------------------------------------------------------------------ > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Msi-workgroups-env-bio-metadata mailing list > >>>>>>>> Msi...@li... > >>>>>>>>=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>>> -- > >>>>>> Susanna-Assunta Sansone, PhD > >>>>>> > >>>>>> NET Project - Coordinator > >>>>>> > >>>>>> www.ebi.ac.uk/net-project > >>>>>> > >>>>>> The European Bioinformatics Institute email: sa...@eb... > >>>>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 > >>>>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > >>>>>> Cambridge CB10 1SD, UK room: A229 > >>>>>> > >>>>> > >>>>> > >>>>>=20 > ------------------------------------------------------------------------ > >>>>>=20 > ------------------------------------------------------------------------- > >>>>> Take Surveys. Earn Cash. Influence the Future of IT > >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to=20 > share your > >>>>> opinions on IT & business topics through brief surveys - and earn= cash > >>>>>=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV > >>>>>=20 > ------------------------------------------------------------------------ > >>>>> _______________________________________________ > >>>>> Msi-workgroups-env-bio-metadata mailing list > >>>>> Msi...@li... > >>>>>=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > >>>> > >>>> -- > >>>> Susanna-Assunta Sansone, PhD > >>>> > >>>> NET Project - Coordinator > >>>> > >>>> www.ebi.ac.uk/net-project > >>>> > >>>> The European Bioinformatics Institute email: sa...@eb... > >>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 > >>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > >>>> Cambridge CB10 1SD, UK room: A229 > >>>> > >>>> > >>>> > >>>>= ------------------------------------------------------------------------ > >>>>=20 > ------------------------------------------------------------------------- > >>>> Take Surveys. Earn Cash. Influence the Future of IT > >>>> Join SourceForge.net's Techsay panel and you'll get the chance to=20 > share your > >>>> opinions on IT & business topics through brief surveys - and earn= cash > >>>>=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV > >>>>= ------------------------------------------------------------------------ > >>>> _______________________________________________ > >>>> Msi-workgroups-env-bio-metadata mailing list > >>>> Msi...@li... > >>>>=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > >>>> > >>> <Env Metab Rep Reqs_v7-SS_OJ.doc> > >>> <UCAM Env Met Use Case.doc> > >>> <UCAM Env Met Real World Example.doc> > >>> <mime-attachment.txt> > >>> <mime-attachment.txt> > >> > >> > > ------------------------------------------------------------------------ > > > >= ------------------------------------------------------------------------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share= =20 > your > > opinions on IT & business topics through brief surveys - and earn cash > >= http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DDE= VDEV > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Msi-workgroups-env-bio-metadata mailing list > > Msi...@li... > >=20 >= https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a > > > > >-- >Dr Norman Morrison >NERC Omic Data Standards Coordinator >Room LF8, School of Computer Science, Kilburn Building, >University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. >Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share= your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DDE= VDEV >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadat= a _______________________________________________ Dr. Mark Viant NERC Advanced Fellow in Metabolomics School of Biosciences The University of Birmingham Birmingham, B15 2TT, U.K. Phone +44-(0)121-414-2219 FAX +44-(0)121-414-5925 http://www.biosciences.bham.ac.uk/labs/viant/ |
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From: Norman M. <mor...@cs...> - 2007-01-05 10:44:26
|
Dear All, This is a very good point. However, taking the big picture view, I think the requirements will continue to evolve and we clearly state this in the paper. I'm about to submit and I think this issue will require further discussion, so I suggest we leave the requirements as they stand and address this point in our online version of the requirements in the near future? All the best, Norman Oliver Jones wrote: > Dear all, > > I think perhaps temperature could be moved to the 'other measured > parameters' section along with pH and organic content but I don't > think it makes a huge difference. > > Oli > > Jake Bundy wrote: >> No major changes at this point (one or two things I would word >> slightly differently is all). >> >> The sole scientific question/suggestion I have is that, under section >> E3.1 (description of terrestrial environment), 'substrate >> temperature' should /not /be a top-level category (maybe this is more >> appropriate for sediment sampling? in which case it shouldn't be >> generalized to all terrestrial environments). But if the majority >> disagree I'm happy to concede this point. >> >> >> jake >> >> >> >> >> ------------------------------------------ >> Dr Jake Bundy >> >> Biomolecular Medicine >> Sir Alexander Fleming Building >> Imperial College >> London SW7 2AZ >> >> j....@im... <mailto:j....@im...> >> >> Tel. +44 (0)20 75943039 >> Fax +44 (0)20 75943226 >> >> >> >> On 4 Jan 2007, at 15:20, Oliver Jones wrote: >> >>> Dear all, >>> >>> I've attached my comments on version 7 of the paper. I think it is >>> pretty much there now and although Susanna made some interesting >>> comments I think they are fairly minor and can be resolved by the >>> editors or maybe even the reviewers. I don't have anything much >>> extra to add at this stage except that I would be in favour of >>> submitting the paper tomorrow as planned. Norman - do we need to >>> suggest reviewers in the cover letter or will Metabolomics do that >>> at their end? >>> >>> My first e-mail this morning may have sounded a little more grumpy >>> then I intended, apologies if so. Please also find attached an >>> updated user case and real world example. These are based on similar >>> but separate metabolomics based studies to avoid it looking like the >>> real world example was retroactively fitted to the standards. >>> >>> I hope this is all OK but if you have any comments please just let >>> me know. >>> >>> Best regards >>> >>> Oli >>> >>> >>> >>> Susanna wrote: >>>> Hi Norman, >>>> >>>> please see page 1-4-9-20 only for some suggestions. >>>> <<Env Metab Rep Reqs_v7-SS.doc>> >>>> >>>> Btw, MIGS is in NBT: http://www.nature.com/nbt/consult/index.html >>>> You have to update the ref ! >>>> >>>> Thanks, >>>> Susanna >>>> >>>> >>>> Norman Morrison wrote: >>>>> Dear All, >>>>> >>>>> Thanks for the info Susanna. It's useful to know that we have an >>>>> extension until Monday/Tuesday next week, but I think our paper is >>>>> basically finished. Actually, I don't know about everyone else, >>>>> but I would prefer to get this paper out of the way and sent off >>>>> tomorrow and would prefer if we stuck to this deadline. >>>>> >>>>> I have received a few separately submitted comments on version 6 - >>>>> so, I've collated these and created version 7. Just in case any of >>>>> you have further comments you would like to add please make them >>>>> on this version (it makes my job a bit easier). >>>>> >>>>> All the best, >>>>> Norman >>>>> >>>>> >>>>> >>>>> Susanna wrote: >>>>>> Hi Norman and All, >>>>>> >>>>>> great job! >>>>>> I suggest not to worry on this too much, as the editors will make >>>>>> such suggestions/changes. >>>>>> >>>>>> Quick note to say that have just called Roy, Chief Editor, and we >>>>>> have still few more days (Monday/Tuesday next week would be fine)!! >>>>>> We/Ontology WG will produce a final version today, so these extra >>>>>> days are key for us. >>>>>> >>>>>> Happy New Year! >>>>>> Susanna >>>>>> >>>>>> Norman Morrison wrote: >>>>>>> Dear All, >>>>>>> >>>>>>> I agree that the use of different fonts is not ideal. >>>>>>> >>>>>>> So far the options seem to be: >>>>>>> >>>>>>> 1) Matt's suggestion that we don't give 'sub-heading' status to >>>>>>> S1 – Description of the …etc. and revert back to italics for >>>>>>> optional items. >>>>>>> 2) Oli's use of colour. I picked up an example copy of >>>>>>> metabolomics at the metaboconf3 and it didn't have any colour in >>>>>>> it. >>>>>>> 3) Felicities use of asterisks'. >>>>>>> >>>>>>> I am happy to go with Matt's suggestion - alternatively we could >>>>>>> leave it as it as and ask the formatting editor of the journal >>>>>>> if they have any advice. I think at this stage it should still >>>>>>> be clear to reviewers what we consider optional. >>>>>>> >>>>>>> Norman >>>>>>> >>>>>>> Matthew Davey wrote: >>>>>>>> Dear all, >>>>>>>> >>>>>>>> I agree with Oli in that the times roman/arial fonts are >>>>>>>> difficult to distinguish. >>>>>>>> >>>>>>>> I have lifted my comment from my previous edited document as >>>>>>>> one solution: >>>>>>>> >>>>>>>> ‘Still not sure about using different fonts to distinguish >>>>>>>> recommended and optional information. Some websites offer html >>>>>>>> download instead of pdf, in which case it will all be in the >>>>>>>> same font. One option is to have the subheadings eg. S1 – >>>>>>>> Description of the … as non-italics as they already standout >>>>>>>> due to the S1 etc code at the start and then have the ‘optional >>>>>>>> information’ bits in italics.’ >>>>>>>> >>>>>>>> Cheers, >>>>>>>> >>>>>>>> Matt >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> *From:* >>>>>>>> msi...@li... >>>>>>>> [mailto:msi...@li...] >>>>>>>> *On Behalf Of *Oliver Jones >>>>>>>> *Sent:* 04 January 2007 10:17 >>>>>>>> *To:* msi...@li... >>>>>>>> *Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version >>>>>>>> 6 - final comments by tomorrow please! >>>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>> First off, a very happy new year to you all. I hope everybody >>>>>>>> enjoyed the holidays? >>>>>>>> >>>>>>>> Right, now to business, swooping in at the very last minute as >>>>>>>> usualy I have a few comments on different things. >>>>>>>> >>>>>>>> >>>>>>>> *1) The paper* >>>>>>>> >>>>>>>> This looks excellent, thanks to everybody for the hard work. I >>>>>>>> hope it is not too late but I'm made a few minor changes and >>>>>>>> comments to version 6 (attached) which I think may be of >>>>>>>> use/interest. In response to Normans question I think the >>>>>>>> following 'optional' form should be left as it is. >>>>>>>> >>>>>>>> o Include details such as the type of housing, for example: >>>>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. >>>>>>>> >>>>>>>> I also agree with Mark and Norman that the merging of >>>>>>>> "description" and "means" is a good idea for now. >>>>>>>> >>>>>>>> My only big worry is the use of the aerial font for optional >>>>>>>> only parameters. I am not sure it shows up that well and I >>>>>>>> personally find it a bit confusing especially if I convert the >>>>>>>> document to a pdf. Unfortunately, I am at a loss at what else >>>>>>>> to suggest except maybe different colours. However, that would >>>>>>>> probably be quite difficult so I think we may just have to go >>>>>>>> with what we have. >>>>>>>> >>>>>>>> *2) Use case/real world examples/project description >>>>>>>> >>>>>>>> *There seems to be some confusion here. When I was formulating >>>>>>>> and commenting on what I thought should be included in the >>>>>>>> requirements I tried to draw on all my experience in >>>>>>>> Environmental Science and metabolomics. Admittedly this may not >>>>>>>> be as extensive as some of the people in the group but I still >>>>>>>> did not draw exclusively from just the one project. To that end >>>>>>>> the described in my user case/real word example/insert your >>>>>>>> description here was not retrofitted to the standards but was >>>>>>>> worked through from the beginning and it took a fair while to >>>>>>>> do. I think this is what Dalibor was trying to do as well. >>>>>>>> (Speaking of Dalibor's examples I spotted a small mistake on >>>>>>>> page 5, under section P5 – Description of acclimation of >>>>>>>> organism(s), in that it still refers to the worms from my >>>>>>>> project. This will need to be changed I think. There are also >>>>>>>> several references in the text but no reference list at the end >>>>>>>> of the document). I think it is very useful to have both user >>>>>>>> cases on the website so people cna see what are proposing that >>>>>>>> they write. >>>>>>>> >>>>>>>> I do take Normans point about why user cases are useful though. >>>>>>>> However, I send round something along those lines several weeks >>>>>>>> ago that was reasonably comprehensive so perhaps we could just >>>>>>>> use that??? However, if you want something more comprehensive I >>>>>>>> am afraid you will have to give me a bit more time to prepare >>>>>>>> it (like an afternoon). Either way please let me know ASAP. >>>>>>>> >>>>>>>> Cheers >>>>>>>> >>>>>>>> Oli >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Mark Viant wrote: >>>>>>>> >>>>>>>> Dear Norm et al >>>>>>>> >>>>>>>> I editted version 5, was about to send, and version 6 appeared! >>>>>>>> So cut/paste my comments into latest version. All minor (except >>>>>>>> you cut a reference). I am happy for this to be sent. Agree >>>>>>>> that merging "description" and "means" is a good idea for now. >>>>>>>> Mark >>>>>>>> >>>>>>>> >>>>>>>> At 13:35 03/01/2007, Norman Morrison wrote: >>>>>>>> >>>>>>>> Dear All, >>>>>>>> >>>>>>>> Please find attached version 6(!) of the paper. I hoped to >>>>>>>> circulate this yesterday but it took a bit longer than I had >>>>>>>> hoped. I think I have now addressed all of the previous issues >>>>>>>> and have commented the sections that I have changed. If you >>>>>>>> feel I have missed anything or any of the issues have not been >>>>>>>> adequately addressed please let me know :-) >>>>>>>> >>>>>>>> There was one issue that I think will require more thought. In >>>>>>>> the process requirement groups there was a motion to merge >>>>>>>> 'Description' and 'Means of' together. In my mind I believed >>>>>>>> that processes should include a concise, 'free text' >>>>>>>> /description/, detailing the specific process that has been >>>>>>>> applied or taken place, and that one should also aim to provide >>>>>>>> a term(s) for the /means/ used (preferably from an ontology or >>>>>>>> CV) in the application of the process. However, 'means' seems >>>>>>>> to be a bit of a vague term, in that the examples we ourselves >>>>>>>> provide, include descriptive terms that mix /actions/ (netted, >>>>>>>> electrically stunned, etc) and /things/ (dry ice, >>>>>>>> formaldehyde). Given this ambiguity, I think it might be best >>>>>>>> if we depricated 'means' for the paper, but I think it will be >>>>>>>> worth revisiting in the next version of the requirements. >>>>>>>> >>>>>>>> At the moment, I have kept the examples in the following >>>>>>>> 'optional' form (see the paper): >>>>>>>> >>>>>>>> o Include details such as the type of housing, for example: >>>>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. >>>>>>>> >>>>>>>> ...or we could just get rid of them altogether. Thoughts? >>>>>>>> >>>>>>>> Hopefully there are not too many more changes to make at this >>>>>>>> late stage, but I welcome your comments. Please can you get >>>>>>>> them back to me by *12pm (GMT) tomorrow* at the latest, so that >>>>>>>> I can incorporate them into the final version for submission. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Norman >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance >>>>>>>> to share your >>>>>>>> opinions on IT & business topics through brief surveys - and >>>>>>>> earn cash >>>>>>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________ >>>>>>>> <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________> >>>>>>>> >>>>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>>>> Msi...@li... >>>>>>>> <mailto:Msi...@li...> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Dr. Mark Viant >>>>>>>> NERC Advanced Fellow in Metabolomics >>>>>>>> School of Biosciences >>>>>>>> The University of Birmingham >>>>>>>> Birmingham, B15 2TT, U.K. >>>>>>>> Phone +44-(0)121-414-2219 >>>>>>>> FAX +44-(0)121-414-5925 >>>>>>>> http://www.biosciences.bham.ac.uk/labs/viant/ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance >>>>>>>> to share your >>>>>>>> opinions on IT & business topics through brief surveys - and >>>>>>>> earn cash >>>>>>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>>>>>>> <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>>>> Msi...@li... >>>>>>>> <mailto:Msi...@li...> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>>>> Join SourceForge.net's Techsay panel and you'll get the chance >>>>>>>> to share your >>>>>>>> opinions on IT & business topics through brief surveys - and >>>>>>>> earn cash >>>>>>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>>>> Msi...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Susanna-Assunta Sansone, PhD >>>>>> >>>>>> NET Project - Coordinator >>>>>> >>>>>> www.ebi.ac.uk/net-project >>>>>> >>>>>> The European Bioinformatics Institute email: sa...@eb... >>>>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 >>>>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >>>>>> Cambridge CB10 1SD, UK room: A229 >>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> ------------------------------------------------------------------------- >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to share your >>>>> opinions on IT & business topics through brief surveys - and earn cash >>>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>>>> ------------------------------------------------------------------------ >>>>> _______________________________________________ >>>>> Msi-workgroups-env-bio-metadata mailing list >>>>> Msi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>>> >>>> -- >>>> Susanna-Assunta Sansone, PhD >>>> >>>> NET Project - Coordinator >>>> >>>> www.ebi.ac.uk/net-project >>>> >>>> The European Bioinformatics Institute email: sa...@eb... >>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 >>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >>>> Cambridge CB10 1SD, UK room: A229 >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> ------------------------------------------------------------------------- >>>> Take Surveys. Earn Cash. Influence the Future of IT >>>> Join SourceForge.net's Techsay panel and you'll get the chance to share your >>>> opinions on IT & business topics through brief surveys - and earn cash >>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>>> ------------------------------------------------------------------------ >>>> _______________________________________________ >>>> Msi-workgroups-env-bio-metadata mailing list >>>> Msi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>>> >>> <Env Metab Rep Reqs_v7-SS_OJ.doc> >>> <UCAM Env Met Use Case.doc> >>> <UCAM Env Met Real World Example.doc> >>> <mime-attachment.txt> >>> <mime-attachment.txt> >> >> > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ------------------------------------------------------------------------ > > _______________________________________________ > Msi-workgroups-env-bio-metadata mailing list > Msi...@li... > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata > -- Dr Norman Morrison NERC Omic Data Standards Coordinator Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 |
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From: Oliver J. <oa...@mo...> - 2007-01-05 09:17:01
|
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Dear all,<br>
<br>
I think perhaps temperature could be moved to the 'other measured
parameters' section along with pH and organic content but I don't think
it makes a huge difference.<br>
<br>
Oli<br>
<br>
Jake Bundy wrote:
<blockquote
cite="mid...@im..."
type="cite">No major changes at this point (one or two things I would
word slightly differently is all).
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</div>
<div><span class="Apple-style-span">The sole scientific
question/suggestion I have is that, under section E3.1 (description of
terrestrial environment), 'substrate temperature' should <i>not </i>be
a top-level category (maybe this is more appropriate for sediment
sampling? in which case it shouldn't be generalized to all terrestrial
environments). But if the majority disagree I'm happy to concede this
point.</span></div>
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</div>
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</div>
<div>jake</div>
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</div>
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</div>
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style="border-collapse: separate; -x-border-x-spacing: 0px; -x-border-y-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>------------------------------------------</div>
<div>Dr Jake Bundy</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Biomolecular Medicine</div>
<div>Sir Alexander Fleming Building</div>
<div>Imperial College</div>
<div>London SW7 2AZ</div>
<div><br class="khtml-block-placeholder">
</div>
<div><a href="mailto:j....@im...">j....@im...</a></div>
<div><br class="khtml-block-placeholder">
</div>
<div>Tel. +44 (0)20 75943039</div>
<div>Fax +44 (0)20 75943226</div>
<div><br class="khtml-block-placeholder">
</div>
<br class="Apple-interchange-newline">
</span></span></span> </div>
<br>
<div>
<div>On 4 Jan 2007, at 15:20, Oliver Jones wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"> Dear all,<br>
<br>
I've attached my comments on version 7 of the paper. I think it is
pretty much there now and although Susanna made some interesting
comments I think they are fairly minor and can be resolved by the
editors or maybe even the reviewers. I don't have anything much extra
to add at this stage except that I would be in favour of submitting the
paper tomorrow as planned. Norman - do we need to suggest reviewers in
the cover letter or will Metabolomics do that at their end?<br>
<br>
My first e-mail this morning may have sounded a little more grumpy then
I intended, apologies if so. Please also find attached an updated user
case and real world example. These are based on similar but separate
metabolomics based studies to avoid it looking like the real world
example was retroactively fitted to the standards.<br>
<br>
I hope this is all OK but if you have any comments please just let me
know.<br>
<br>
Best regards<br>
<br>
Oli<br>
<br>
<br>
<br>
Susanna wrote:
<blockquote cite="mid...@eb..." type="cite"> Hi
Norman,<br>
<br>
please see page 1-4-9-20 only for some suggestions.<br>
<<Env Metab Rep Reqs_v7-SS.doc>><br>
<br>
Btw, MIGS is in NBT: <a class="moz-txt-link-freetext"
href="http://www.nature.com/nbt/consult/index.html">http://www.nature.com/nbt/consult/index.html</a><br>
You have to update the ref !<br>
<br>
Thanks,<br>
Susanna<br>
<br>
<br>
Norman Morrison wrote:<br>
<blockquote type="cite" cite="mid...@cs...">Dear
All, <br>
<br>
Thanks for the info Susanna. It's useful to know that we have an
extension until Monday/Tuesday next week, but I think our paper is
basically finished. Actually, I don't know about everyone else, but I
would prefer to get this paper out of the way and sent off tomorrow and
would prefer if we stuck to this deadline. <br>
<br>
I have received a few separately submitted comments on version 6 - so,
I've collated these and created version 7. Just in case any of you have
further comments you would like to add please make them on this version
(it makes my job a bit easier). <br>
<br>
All the best, <br>
Norman <br>
<br>
<br>
<br>
Susanna wrote: <br>
<blockquote type="cite">Hi Norman and All, <br>
<br>
great job! <br>
I suggest not to worry on this too much, as the editors will make such
suggestions/changes. <br>
<br>
Quick note to say that have just called Roy, Chief Editor, and we have
still few more days (Monday/Tuesday next week would be fine)!! <br>
We/Ontology WG will produce a final version today, so these extra days
are key for us. <br>
<br>
Happy New Year! <br>
Susanna <br>
<br>
Norman Morrison wrote: <br>
<blockquote type="cite">Dear All, <br>
<br>
I agree that the use of different fonts is not ideal. <br>
<br>
So far the options seem to be: <br>
<br>
1) Matt's suggestion that we don't give 'sub-heading' status to S1 –
Description of the …etc. and revert back to italics for optional items.
<br>
2) Oli's use of colour. I picked up an example copy of metabolomics at
the metaboconf3 and it didn't have any colour in it. <br>
3) Felicities use of asterisks'. <br>
<br>
I am happy to go with Matt's suggestion - alternatively we could leave
it as it as and ask the formatting editor of the journal if they have
any advice. I think at this stage it should still be clear to reviewers
what we consider optional. <br>
<br>
Norman <br>
<br>
Matthew Davey wrote: <br>
<blockquote type="cite">Dear all, <br>
<br>
I agree with Oli in that the times roman/arial fonts are difficult to
distinguish. <br>
<br>
I have lifted my comment from my previous edited document as one
solution: <br>
<br>
‘Still not sure about using different fonts to distinguish recommended
and optional information. Some websites offer html download instead of
pdf, in which case it will all be in the same font. One option is to
have the subheadings eg. S1 – Description of the … as non-italics as
they already standout due to the S1 etc code at the start and then have
the ‘optional information’ bits in italics.’ <br>
<br>
Cheers, <br>
<br>
Matt <br>
<br>
------------------------------------------------------------------------
<br>
<br>
*From:* <a class="moz-txt-link-abbreviated"
href="mailto:msi...@li...">msi...@li...</a>
[<a class="moz-txt-link-freetext"
href="mailto:msi...@li...">mailto:msi...@li...</a>]
*On Behalf Of *Oliver Jones <br>
*Sent:* 04 January 2007 10:17 <br>
*To:* <a class="moz-txt-link-abbreviated"
href="mailto:msi...@li...">msi...@li...</a>
<br>
*Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version 6 -
final comments by tomorrow please! <br>
<br>
Dear all, <br>
<br>
First off, a very happy new year to you all. I hope everybody enjoyed
the holidays? <br>
<br>
Right, now to business, swooping in at the very last minute as usualy I
have a few comments on different things. <br>
<br>
<br>
*1) The paper* <br>
<br>
This looks excellent, thanks to everybody for the hard work. I hope it
is not too late but I'm made a few minor changes and comments to
version 6 (attached) which I think may be of use/interest. In response
to Normans question I think the following 'optional' form should be
left as it is. <br>
<br>
o Include details such as the type of housing, for example: Cage,
aquaria, continuous culture, seed bag or plant pot etc. <br>
<br>
I also agree with Mark and Norman that the merging of "description" and
"means" is a good idea for now. <br>
<br>
My only big worry is the use of the aerial font for optional only
parameters. I am not sure it shows up that well and I personally find
it a bit confusing especially if I convert the document to a pdf.
Unfortunately, I am at a loss at what else to suggest except maybe
different colours. However, that would probably be quite difficult so I
think we may just have to go with what we have. <br>
<br>
*2) Use case/real world examples/project description <br>
<br>
*There seems to be some confusion here. When I was formulating and
commenting on what I thought should be included in the requirements I
tried to draw on all my experience in Environmental Science and
metabolomics. Admittedly this may not be as extensive as some of the
people in the group but I still did not draw exclusively from just the
one project. To that end the described in my user case/real word
example/insert your description here was not retrofitted to the
standards but was worked through from the beginning and it took a fair
while to do. I think this is what Dalibor was trying to do as well.
(Speaking of Dalibor's examples I spotted a small mistake on page 5,
under section P5 – Description of acclimation of organism(s), in that
it still refers to the worms from my project. This will need to be
changed I think. There are also several references in the text but no
reference list at the end of the document). I think it is very useful
to have both user cases on the website so people cna see what are
proposing that they write. <br>
<br>
I do take Normans point about why user cases are useful though.
However, I send round something along those lines several weeks ago
that was reasonably comprehensive so perhaps we could just use that???
However, if you want something more comprehensive I am afraid you will
have to give me a bit more time to prepare it (like an afternoon).
Either way please let me know ASAP. <br>
<br>
Cheers <br>
<br>
Oli <br>
<br>
<br>
<br>
<br>
<br>
Mark Viant wrote: <br>
<br>
Dear Norm et al <br>
<br>
I editted version 5, was about to send, and version 6 appeared! So
cut/paste my comments into latest version. All minor (except you cut a
reference). I am happy for this to be sent. Agree that merging
"description" and "means" is a good idea for now. <br>
Mark <br>
<br>
<br>
At 13:35 03/01/2007, Norman Morrison wrote: <br>
<br>
Dear All, <br>
<br>
Please find attached version 6(!) of the paper. I hoped to circulate
this yesterday but it took a bit longer than I had hoped. I think I
have now addressed all of the previous issues and have commented the
sections that I have changed. If you feel I have missed anything or any
of the issues have not been adequately addressed please let me know :-)
<br>
<br>
There was one issue that I think will require more thought. In the
process requirement groups there was a motion to merge 'Description'
and 'Means of' together. In my mind I believed that processes should
include a concise, 'free text' /description/, detailing the specific
process that has been applied or taken place, and that one should also
aim to provide a term(s) for the /means/ used (preferably from an
ontology or CV) in the application of the process. However, 'means'
seems to be a bit of a vague term, in that the examples we ourselves
provide, include descriptive terms that mix /actions/ (netted,
electrically stunned, etc) and /things/ (dry ice, formaldehyde). Given
this ambiguity, I think it might be best if we depricated 'means' for
the paper, but I think it will be worth revisiting in the next version
of the requirements. <br>
<br>
At the moment, I have kept the examples in the following 'optional'
form (see the paper): <br>
<br>
o Include details such as the type of housing, for example: Cage,
aquaria, continuous culture, seed bag or plant pot etc. <br>
<br>
...or we could just get rid of them altogether. Thoughts? <br>
<br>
Hopefully there are not too many more changes to make at this late
stage, but I welcome your comments. Please can you get them back to me
by *12pm (GMT) tomorrow* at the latest, so that I can incorporate them
into the final version for submission. <br>
<br>
Thanks, <br>
Norman <br>
<br>
<br>
<br>
<br>
<br>
<br>
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School of Biosciences <br>
The University of Birmingham <br>
Birmingham, B15 2TT, U.K. <br>
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FAX +44-(0)121-414-5925 <br>
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-- <br>
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<br>
NET Project - Coordinator <br>
<br>
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class="moz-txt-link-abbreviated" href="mailto:sa...@eb...">sa...@eb...</a>
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<pre class="moz-signature" cols="$mailwrapcol">--
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NET Project - Coordinator
<a class="moz-txt-link-abbreviated"
href="http://www.ebi.ac.uk/net-project">www.ebi.ac.uk/net-project</a>
The European Bioinformatics Institute email: <a
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EMBL Outstation - Hinxton direct: +44 (0)1223 494 691
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</blockquote>
<span>
<div><Env Metab Rep Reqs_v7-SS_OJ.doc></div>
</span><span>
<div><UCAM Env Met Use Case.doc></div>
</span><span>
<div><UCAM Env Met Real World Example.doc></div>
</span><span>
<div><mime-attachment.txt></div>
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<div><mime-attachment.txt></div>
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|
|
From: Jake B. <j....@im...> - 2007-01-04 18:22:32
|
No major changes at this point (one or two things I would word =20 slightly differently is all). The sole scientific question/suggestion I have is that, under section =20= E3.1 (description of terrestrial environment), 'substrate =20 temperature' should not be a top-level category (maybe this is more =20 appropriate for sediment sampling? in which case it shouldn't be =20 generalized to all terrestrial environments). But if the majority =20 disagree I'm happy to concede this point. jake ------------------------------------------ Dr Jake Bundy Biomolecular Medicine Sir Alexander Fleming Building Imperial College London SW7 2AZ j....@im... Tel. +44 (0)20 75943039 Fax +44 (0)20 75943226 On 4 Jan 2007, at 15:20, Oliver Jones wrote: > Dear all, > > I've attached my comments on version 7 of the paper. I think it is =20 > pretty much there now and although Susanna made some interesting =20 > comments I think they are fairly minor and can be resolved by the =20 > editors or maybe even the reviewers. I don't have anything much =20 > extra to add at this stage except that I would be in favour of =20 > submitting the paper tomorrow as planned. Norman - do we need to =20 > suggest reviewers in the cover letter or will Metabolomics do that =20 > at their end? > > My first e-mail this morning may have sounded a little more grumpy =20 > then I intended, apologies if so. Please also find attached an =20 > updated user case and real world example. These are based on =20 > similar but separate metabolomics based studies to avoid it looking =20= > like the real world example was retroactively fitted to the standards. > > I hope this is all OK but if you have any comments please just let =20 > me know. > > Best regards > > Oli > > > > Susanna wrote: >> Hi Norman, >> >> please see page 1-4-9-20 only for some suggestions. >> <<Env Metab Rep Reqs_v7-SS.doc>> >> >> Btw, MIGS is in NBT: http://www.nature.com/nbt/consult/index.html >> You have to update the ref ! >> >> Thanks, >> Susanna >> >> >> Norman Morrison wrote: >>> Dear All, >>> >>> Thanks for the info Susanna. It's useful to know that we have an =20= >>> extension until Monday/Tuesday next week, but I think our paper =20 >>> is basically finished. Actually, I don't know about everyone =20 >>> else, but I would prefer to get this paper out of the way and =20 >>> sent off tomorrow and would prefer if we stuck to this deadline. >>> >>> I have received a few separately submitted comments on version 6 =20 >>> - so, I've collated these and created version 7. Just in case any =20= >>> of you have further comments you would like to add please make =20 >>> them on this version (it makes my job a bit easier). >>> >>> All the best, >>> Norman >>> >>> >>> >>> Susanna wrote: >>>> Hi Norman and All, >>>> >>>> great job! >>>> I suggest not to worry on this too much, as the editors will =20 >>>> make such suggestions/changes. >>>> >>>> Quick note to say that have just called Roy, Chief Editor, and =20 >>>> we have still few more days (Monday/Tuesday next week would be =20 >>>> fine)!! >>>> We/Ontology WG will produce a final version today, so these =20 >>>> extra days are key for us. >>>> >>>> Happy New Year! >>>> Susanna >>>> >>>> Norman Morrison wrote: >>>>> Dear All, >>>>> >>>>> I agree that the use of different fonts is not ideal. >>>>> >>>>> So far the options seem to be: >>>>> >>>>> 1) Matt's suggestion that we don't give 'sub-heading' status to =20= >>>>> S1 =96 Description of the =85etc. and revert back to italics for =20= >>>>> optional items. >>>>> 2) Oli's use of colour. I picked up an example copy of =20 >>>>> metabolomics at the metaboconf3 and it didn't have any colour =20 >>>>> in it. >>>>> 3) Felicities use of asterisks'. >>>>> >>>>> I am happy to go with Matt's suggestion - alternatively we =20 >>>>> could leave it as it as and ask the formatting editor of the =20 >>>>> journal if they have any advice. I think at this stage it =20 >>>>> should still be clear to reviewers what we consider optional. >>>>> >>>>> Norman >>>>> >>>>> Matthew Davey wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I agree with Oli in that the times roman/arial fonts are =20 >>>>>> difficult to distinguish. >>>>>> >>>>>> I have lifted my comment from my previous edited document as =20 >>>>>> one solution: >>>>>> >>>>>> =91Still not sure about using different fonts to distinguish =20 >>>>>> recommended and optional information. Some websites offer html =20= >>>>>> download instead of pdf, in which case it will all be in the =20 >>>>>> same font. One option is to have the subheadings eg. S1 =96 =20 >>>>>> Description of the =85 as non-italics as they already standout =20= >>>>>> due to the S1 etc code at the start and then have the =20 >>>>>> =91optional information=92 bits in italics.=92 >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Matt >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> ------- >>>>>> >>>>>> *From:* msi-workgroups-env-bio-metadata-=20 >>>>>> bo...@li... [mailto:msi-workgroups-env-bio-=20 >>>>>> met...@li...] *On Behalf Of *Oliver =20 >>>>>> Jones >>>>>> *Sent:* 04 January 2007 10:17 >>>>>> *To:* msi...@li... >>>>>> *Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version =20= >>>>>> 6 - final comments by tomorrow please! >>>>>> >>>>>> Dear all, >>>>>> >>>>>> First off, a very happy new year to you all. I hope everybody =20 >>>>>> enjoyed the holidays? >>>>>> >>>>>> Right, now to business, swooping in at the very last minute as =20= >>>>>> usualy I have a few comments on different things. >>>>>> >>>>>> >>>>>> *1) The paper* >>>>>> >>>>>> This looks excellent, thanks to everybody for the hard work. I =20= >>>>>> hope it is not too late but I'm made a few minor changes and =20 >>>>>> comments to version 6 (attached) which I think may be of use/=20 >>>>>> interest. In response to Normans question I think the =20 >>>>>> following 'optional' form should be left as it is. >>>>>> >>>>>> o Include details such as the type of housing, for example: =20 >>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. >>>>>> >>>>>> I also agree with Mark and Norman that the merging of =20 >>>>>> "description" and "means" is a good idea for now. >>>>>> >>>>>> My only big worry is the use of the aerial font for optional =20 >>>>>> only parameters. I am not sure it shows up that well and I =20 >>>>>> personally find it a bit confusing especially if I convert the =20= >>>>>> document to a pdf. Unfortunately, I am at a loss at what else =20 >>>>>> to suggest except maybe different colours. However, that would =20= >>>>>> probably be quite difficult so I think we may just have to go =20 >>>>>> with what we have. >>>>>> >>>>>> *2) Use case/real world examples/project description >>>>>> >>>>>> *There seems to be some confusion here. When I was formulating =20= >>>>>> and commenting on what I thought should be included in the =20 >>>>>> requirements I tried to draw on all my experience in =20 >>>>>> Environmental Science and metabolomics. Admittedly this may =20 >>>>>> not be as extensive as some of the people in the group but I =20 >>>>>> still did not draw exclusively from just the one project. To =20 >>>>>> that end the described in my user case/real word example/=20 >>>>>> insert your description here was not retrofitted to the =20 >>>>>> standards but was worked through from the beginning and it =20 >>>>>> took a fair while to do. I think this is what Dalibor was =20 >>>>>> trying to do as well. (Speaking of Dalibor's examples I =20 >>>>>> spotted a small mistake on page 5, under section P5 =96 =20 >>>>>> Description of acclimation of organism(s), in that it still =20 >>>>>> refers to the worms from my project. This will need to be =20 >>>>>> changed I think. There are also several references in the text =20= >>>>>> but no reference list at the end of the document). I think it =20 >>>>>> is very useful to have both user cases on the website so =20 >>>>>> people cna see what are proposing that they write. >>>>>> >>>>>> I do take Normans point about why user cases are useful =20 >>>>>> though. However, I send round something along those lines =20 >>>>>> several weeks ago that was reasonably comprehensive so perhaps =20= >>>>>> we could just use that??? However, if you want something more =20 >>>>>> comprehensive I am afraid you will have to give me a bit more =20 >>>>>> time to prepare it (like an afternoon). Either way please let =20 >>>>>> me know ASAP. >>>>>> >>>>>> Cheers >>>>>> >>>>>> Oli >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Mark Viant wrote: >>>>>> >>>>>> Dear Norm et al >>>>>> >>>>>> I editted version 5, was about to send, and version 6 =20 >>>>>> appeared! So cut/paste my comments into latest version. All =20 >>>>>> minor (except you cut a reference). I am happy for this to be =20 >>>>>> sent. Agree that merging "description" and "means" is a good =20 >>>>>> idea for now. >>>>>> Mark >>>>>> >>>>>> >>>>>> At 13:35 03/01/2007, Norman Morrison wrote: >>>>>> >>>>>> Dear All, >>>>>> >>>>>> Please find attached version 6(!) of the paper. I hoped to =20 >>>>>> circulate this yesterday but it took a bit longer than I had =20 >>>>>> hoped. I think I have now addressed all of the previous issues =20= >>>>>> and have commented the sections that I have changed. If you =20 >>>>>> feel I have missed anything or any of the issues have not been =20= >>>>>> adequately addressed please let me know :-) >>>>>> >>>>>> There was one issue that I think will require more thought. In =20= >>>>>> the process requirement groups there was a motion to merge =20 >>>>>> 'Description' and 'Means of' together. In my mind I believed =20 >>>>>> that processes should include a concise, 'free text' /=20 >>>>>> description/, detailing the specific process that has been =20 >>>>>> applied or taken place, and that one should also aim to =20 >>>>>> provide a term(s) for the /means/ used (preferably from an =20 >>>>>> ontology or CV) in the application of the process. However, =20 >>>>>> 'means' seems to be a bit of a vague term, in that the =20 >>>>>> examples we ourselves provide, include descriptive terms that =20 >>>>>> mix /actions/ (netted, electrically stunned, etc) and /things/ =20= >>>>>> (dry ice, formaldehyde). Given this ambiguity, I think it =20 >>>>>> might be best if we depricated 'means' for the paper, but I =20 >>>>>> think it will be worth revisiting in the next version of the =20 >>>>>> requirements. >>>>>> >>>>>> At the moment, I have kept the examples in the following =20 >>>>>> 'optional' form (see the paper): >>>>>> >>>>>> o Include details such as the type of housing, for example: =20 >>>>>> Cage, aquaria, continuous culture, seed bag or plant pot etc. >>>>>> >>>>>> ...or we could just get rid of them altogether. Thoughts? >>>>>> >>>>>> Hopefully there are not too many more changes to make at this =20 >>>>>> late stage, but I welcome your comments. Please can you get =20 >>>>>> them back to me by *12pm (GMT) tomorrow* at the latest, so =20 >>>>>> that I can incorporate them into the final version for =20 >>>>>> submission. >>>>>> >>>>>> Thanks, >>>>>> Norman >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> -------- >>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>> Join SourceForge.net's Techsay panel and you'll get the chance =20= >>>>>> to share your >>>>>> opinions on IT & business topics through brief surveys - and =20 >>>>>> earn cash >>>>>> http://www.techsay.com/default.php?=20 >>>>>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV_______________________= ____=20 >>>>>> ____________________ <http://www.techsay.com/default.php?=20 >>>>>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV_______________________= ____=20 >>>>>> ____________________> >>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>> Msi...@li... =20 >>>>>> <mailto:Msi...@li...> >>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-=20 >>>>>> env-bio-metadata >>>>>> >>>>>> _______________________________________________ >>>>>> Dr. Mark Viant >>>>>> NERC Advanced Fellow in Metabolomics >>>>>> School of Biosciences >>>>>> The University of Birmingham >>>>>> Birmingham, B15 2TT, U.K. >>>>>> Phone +44-(0)121-414-2219 >>>>>> FAX +44-(0)121-414-5925 >>>>>> http://www.biosciences.bham.ac.uk/labs/viant/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> ------- >>>>>> >>>>>> >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> -------- >>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>> Join SourceForge.net's Techsay panel and you'll get the chance =20= >>>>>> to share your >>>>>> opinions on IT & business topics through brief surveys - and =20 >>>>>> earn cash >>>>>> http://www.techsay.com/default.php?=20 >>>>>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV = <http://www.techsay.com/=20 >>>>>> default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV> >>>>>> >>>>>> >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> ------- >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>> Msi...@li... =20 >>>>>> <mailto:Msi...@li...> >>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-=20 >>>>>> env-bio-metadata >>>>>> =20 >>>>>> -----------------------------------------------------------------=20= >>>>>> ------- >>>>>> >>>>>> -----------------------------------------------------------------=20= >>>>>> -------- >>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>> Join SourceForge.net's Techsay panel and you'll get the chance =20= >>>>>> to share your >>>>>> opinions on IT & business topics through brief surveys - and =20 >>>>>> earn cash >>>>>> http://www.techsay.com/default.php?=20 >>>>>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >>>>>> -----------------------------------------------------------------=20= >>>>>> ------- >>>>>> >>>>>> _______________________________________________ >>>>>> Msi-workgroups-env-bio-metadata mailing list >>>>>> Msi...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-=20 >>>>>> env-bio-metadata >>>>>> >>>>> >>>>> >>>>> >>>> >>>> --=20 >>>> Susanna-Assunta Sansone, PhD >>>> >>>> NET Project - Coordinator >>>> >>>> www.ebi.ac.uk/net-project >>>> >>>> The European Bioinformatics Institute email: sa...@eb... >>>> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 >>>> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >>>> Cambridge CB10 1SD, UK room: A229 >>>> >>> >>> >>> --------------------------------------------------------------------=20= >>> ----- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to =20= >>> share your >>> opinions on IT & business topics through brief surveys - and earn =20= >>> cash >>> http://www.techsay.com/default.php?=20 >>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >>> _______________________________________________ >>> Msi-workgroups-env-bio-metadata mailing list >>> Msi...@li... >>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-=20 >>> bio-metadata >> >> --=20 >> Susanna-Assunta Sansone, PhD >> >> NET Project - Coordinator >> >> www.ebi.ac.uk/net-project >> =09 >> The European Bioinformatics Institute email: sa...@eb... >> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 >> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >> Cambridge CB10 1SD, UK room: A229 >> >> >> >> ---------------------------------------------------------------------=20= >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >> share your >> opinions on IT & business topics through brief surveys - and earn =20 >> cash >> http://www.techsay.com/default.php?=20 >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >> _______________________________________________ >> Msi-workgroups-env-bio-metadata mailing list >> Msi...@li... >> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-=20 >> bio-metadata >> > <Env Metab Rep Reqs_v7-SS_OJ.doc> > <UCAM Env Met Use Case.doc> > <UCAM Env Met Real World Example.doc> > <mime-attachment.txt> > <mime-attachment.txt> |
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From: Oliver J. <oa...@mo...> - 2007-01-04 15:20:28
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Dear all,<br> <br> I've attached my comments on version 7 of the paper. I think it is pretty much there now and although Susanna made some interesting comments I think they are fairly minor and can be resolved by the editors or maybe even the reviewers. I don't have anything much extra to add at this stage except that I would be in favour of submitting the paper tomorrow as planned. Norman - do we need to suggest reviewers in the cover letter or will Metabolomics do that at their end?<br> <br> My first e-mail this morning may have sounded a little more grumpy then I intended, apologies if so. Please also find attached an updated user case and real world example. These are based on similar but separate metabolomics based studies to avoid it looking like the real world example was retroactively fitted to the standards.<br> <br> I hope this is all OK but if you have any comments please just let me know.<br> <br> Best regards<br> <br> Oli<br> <br> <br> <br> Susanna wrote: <blockquote cite="mid...@eb..." type="cite"> <title></title> Hi Norman,<br> <br> please see page 1-4-9-20 only for some suggestions.<br> <<Env Metab Rep Reqs_v7-SS.doc>><br> <br> Btw, MIGS is in NBT: <a class="moz-txt-link-freetext" href="http://www.nature.com/nbt/consult/index.html">http://www.nature.com/nbt/consult/index.html</a><br> You have to update the ref !<br> <br> Thanks,<br> Susanna<br> <br> <br> Norman Morrison wrote:<br> <blockquote type="cite" cite="mid...@cs...">Dear All, <br> <br> Thanks for the info Susanna. It's useful to know that we have an extension until Monday/Tuesday next week, but I think our paper is basically finished. Actually, I don't know about everyone else, but I would prefer to get this paper out of the way and sent off tomorrow and would prefer if we stuck to this deadline. <br> <br> I have received a few separately submitted comments on version 6 - so, I've collated these and created version 7. Just in case any of you have further comments you would like to add please make them on this version (it makes my job a bit easier). <br> <br> All the best, <br> Norman <br> <br> <br> <br> Susanna wrote: <br> <blockquote type="cite">Hi Norman and All, <br> <br> great job! <br> I suggest not to worry on this too much, as the editors will make such suggestions/changes. <br> <br> Quick note to say that have just called Roy, Chief Editor, and we have still few more days (Monday/Tuesday next week would be fine)!! <br> We/Ontology WG will produce a final version today, so these extra days are key for us. <br> <br> Happy New Year! <br> Susanna <br> <br> Norman Morrison wrote: <br> <blockquote type="cite">Dear All, <br> <br> I agree that the use of different fonts is not ideal. <br> <br> So far the options seem to be: <br> <br> 1) Matt's suggestion that we don't give 'sub-heading' status to S1 – Description of the …etc. and revert back to italics for optional items. <br> 2) Oli's use of colour. I picked up an example copy of metabolomics at the metaboconf3 and it didn't have any colour in it. <br> 3) Felicities use of asterisks'. <br> <br> I am happy to go with Matt's suggestion - alternatively we could leave it as it as and ask the formatting editor of the journal if they have any advice. I think at this stage it should still be clear to reviewers what we consider optional. <br> <br> Norman <br> <br> Matthew Davey wrote: <br> <blockquote type="cite">Dear all, <br> <br> I agree with Oli in that the times roman/arial fonts are difficult to distinguish. <br> <br> I have lifted my comment from my previous edited document as one solution: <br> <br> ‘Still not sure about using different fonts to distinguish recommended and optional information. Some websites offer html download instead of pdf, in which case it will all be in the same font. One option is to have the subheadings eg. S1 – Description of the … as non-italics as they already standout due to the S1 etc code at the start and then have the ‘optional information’ bits in italics.’ <br> <br> Cheers, <br> <br> Matt <br> <br> ------------------------------------------------------------------------ <br> <br> *From:* <a class="moz-txt-link-abbreviated" href="mailto:msi...@li...">msi...@li...</a> [<a class="moz-txt-link-freetext" href="mailto:msi...@li...">mailto:msi...@li...</a>] *On Behalf Of *Oliver Jones <br> *Sent:* 04 January 2007 10:17 <br> *To:* <a class="moz-txt-link-abbreviated" href="mailto:msi...@li...">msi...@li...</a> <br> *Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version 6 - final comments by tomorrow please! <br> <br> Dear all, <br> <br> First off, a very happy new year to you all. I hope everybody enjoyed the holidays? <br> <br> Right, now to business, swooping in at the very last minute as usualy I have a few comments on different things. <br> <br> <br> *1) The paper* <br> <br> This looks excellent, thanks to everybody for the hard work. I hope it is not too late but I'm made a few minor changes and comments to version 6 (attached) which I think may be of use/interest. In response to Normans question I think the following 'optional' form should be left as it is. <br> <br> o Include details such as the type of housing, for example: Cage, aquaria, continuous culture, seed bag or plant pot etc. <br> <br> I also agree with Mark and Norman that the merging of "description" and "means" is a good idea for now. <br> <br> My only big worry is the use of the aerial font for optional only parameters. I am not sure it shows up that well and I personally find it a bit confusing especially if I convert the document to a pdf. Unfortunately, I am at a loss at what else to suggest except maybe different colours. However, that would probably be quite difficult so I think we may just have to go with what we have. <br> <br> *2) Use case/real world examples/project description <br> <br> *There seems to be some confusion here. When I was formulating and commenting on what I thought should be included in the requirements I tried to draw on all my experience in Environmental Science and metabolomics. Admittedly this may not be as extensive as some of the people in the group but I still did not draw exclusively from just the one project. To that end the described in my user case/real word example/insert your description here was not retrofitted to the standards but was worked through from the beginning and it took a fair while to do. I think this is what Dalibor was trying to do as well. (Speaking of Dalibor's examples I spotted a small mistake on page 5, under section P5 – Description of acclimation of organism(s), in that it still refers to the worms from my project. This will need to be changed I think. There are also several references in the text but no reference list at the end of the document). I think it is very useful to have both user cases on the website so people cna see what are proposing that they write. <br> <br> I do take Normans point about why user cases are useful though. However, I send round something along those lines several weeks ago that was reasonably comprehensive so perhaps we could just use that??? However, if you want something more comprehensive I am afraid you will have to give me a bit more time to prepare it (like an afternoon). Either way please let me know ASAP. <br> <br> Cheers <br> <br> Oli <br> <br> <br> <br> <br> <br> Mark Viant wrote: <br> <br> Dear Norm et al <br> <br> I editted version 5, was about to send, and version 6 appeared! So cut/paste my comments into latest version. All minor (except you cut a reference). I am happy for this to be sent. Agree that merging "description" and "means" is a good idea for now. <br> Mark <br> <br> <br> At 13:35 03/01/2007, Norman Morrison wrote: <br> <br> Dear All, <br> <br> Please find attached version 6(!) of the paper. I hoped to circulate this yesterday but it took a bit longer than I had hoped. I think I have now addressed all of the previous issues and have commented the sections that I have changed. If you feel I have missed anything or any of the issues have not been adequately addressed please let me know :-) <br> <br> There was one issue that I think will require more thought. In the process requirement groups there was a motion to merge 'Description' and 'Means of' together. In my mind I believed that processes should include a concise, 'free text' /description/, detailing the specific process that has been applied or taken place, and that one should also aim to provide a term(s) for the /means/ used (preferably from an ontology or CV) in the application of the process. However, 'means' seems to be a bit of a vague term, in that the examples we ourselves provide, include descriptive terms that mix /actions/ (netted, electrically stunned, etc) and /things/ (dry ice, formaldehyde). Given this ambiguity, I think it might be best if we depricated 'means' for the paper, but I think it will be worth revisiting in the next version of the requirements. <br> <br> At the moment, I have kept the examples in the following 'optional' form (see the paper): <br> <br> o Include details such as the type of housing, for example: Cage, aquaria, continuous culture, seed bag or plant pot etc. <br> <br> ...or we could just get rid of them altogether. Thoughts? <br> <br> Hopefully there are not too many more changes to make at this late stage, but I welcome your comments. Please can you get them back to me by *12pm (GMT) tomorrow* at the latest, so that I can incorporate them into the final version for submission. <br> <br> Thanks, <br> Norman <br> <br> <br> <br> <br> <br> <br> <br> ------------------------------------------------------------------------- <br> Take Surveys. Earn Cash. Influence the Future of IT <br> Join SourceForge.net's Techsay panel and you'll get the chance to share your <br> opinions on IT & business topics through brief surveys - and earn cash <br> <a class="moz-txt-link-freetext" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________">http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________</a> <a class="moz-txt-link-rfc2396E" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________"><http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________></a> <br> Msi-workgroups-env-bio-metadata mailing list <br> <a class="moz-txt-link-abbreviated" href="mailto:Msi...@li...">Msi...@li...</a> <a class="moz-txt-link-rfc2396E" href="mailto:Msi...@li..."><mailto:Msi...@li...></a> <br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata">https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata</a> <br> <br> _______________________________________________ <br> Dr. Mark Viant <br> NERC Advanced Fellow in Metabolomics <br> School of Biosciences <br> The University of Birmingham <br> Birmingham, B15 2TT, U.K. <br> Phone +44-(0)121-414-2219 <br> FAX +44-(0)121-414-5925 <br> <a class="moz-txt-link-freetext" href="http://www.biosciences.bham.ac.uk/labs/viant/">http://www.biosciences.bham.ac.uk/labs/viant/</a> <br> <br> <br> <br> <br> ------------------------------------------------------------------------ <br> <br> <br> <br> ------------------------------------------------------------------------- <br> Take Surveys. Earn Cash. Influence the Future of IT <br> Join SourceForge.net's Techsay panel and you'll get the chance to share your <br> opinions on IT & business topics through brief surveys - and earn cash <br> <a class="moz-txt-link-freetext" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV">http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV</a> <a class="moz-txt-link-rfc2396E" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV"><http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV></a> <br> <br> <br> <br> ------------------------------------------------------------------------ <br> <br> <br> <br> _______________________________________________ <br> Msi-workgroups-env-bio-metadata mailing list <br> <a class="moz-txt-link-abbreviated" href="mailto:Msi...@li...">Msi...@li...</a> <a class="moz-txt-link-rfc2396E" href="mailto:Msi...@li..."><mailto:Msi...@li...></a> <br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata">https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata</a> <br> ------------------------------------------------------------------------ <br> <br> ------------------------------------------------------------------------- <br> Take Surveys. Earn Cash. Influence the Future of IT <br> Join SourceForge.net's Techsay panel and you'll get the chance to share your <br> opinions on IT & business topics through brief surveys - and earn cash <br> <a class="moz-txt-link-freetext" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV">http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV</a> <br> ------------------------------------------------------------------------ <br> <br> _______________________________________________ <br> Msi-workgroups-env-bio-metadata mailing list <br> <a class="moz-txt-link-abbreviated" href="mailto:Msi...@li...">Msi...@li...</a> <br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata">https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata</a> <br> </blockquote> <br> <br> </blockquote> <br> -- <br> Susanna-Assunta Sansone, PhD <br> <br> NET Project - Coordinator <br> <br> <a class="moz-txt-link-abbreviated" href="http://www.ebi.ac.uk/net-project">www.ebi.ac.uk/net-project</a> <br> <br> The European Bioinformatics Institute <a class="moz-txt-link-freetext" href="email:%A0">email: </a> <a class="moz-txt-link-abbreviated" href="mailto:sa...@eb...">sa...@eb...</a> <br> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 <br> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 <br> Cambridge CB10 1SD, UK room: A229 <br> <br> </blockquote> <br> <br> <pre wrap=""><hr size="4" width="90%"> ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash <a class="moz-txt-link-freetext" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV">http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV</a></pre> <pre wrap=""><hr size="4" width="90%"> _______________________________________________ Msi-workgroups-env-bio-metadata mailing list <a class="moz-txt-link-abbreviated" href="mailto:Msi...@li...">Msi...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata">https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata</a></pre> </blockquote> <br> <pre class="moz-signature" cols="$mailwrapcol">-- Susanna-Assunta Sansone, PhD NET Project - Coordinator <a class="moz-txt-link-abbreviated" href="http://www.ebi.ac.uk/net-project">www.ebi.ac.uk/net-project</a> The European Bioinformatics Institute email: <a class="moz-txt-link-abbreviated" href="mailto:sa...@eb...">sa...@eb...</a> EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK room: A229 </pre> <br> <pre wrap=""> <hr size="4" width="90%"> ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash <a class="moz-txt-link-freetext" href="http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV">http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV</a></pre> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ Msi-workgroups-env-bio-metadata mailing list <a class="moz-txt-link-abbreviated" href="mailto:Msi...@li...">Msi...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata">https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata</a> </pre> </blockquote> </body> </html> |
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From: Norman M. <mor...@cs...> - 2007-01-04 14:15:25
|
Dear All, Thanks for the info Susanna. It's useful to know that we have an extension until Monday/Tuesday next week, but I think our paper is basically finished. Actually, I don't know about everyone else, but I would prefer to get this paper out of the way and sent off tomorrow and would prefer if we stuck to this deadline. I have received a few separately submitted comments on version 6 - so, I've collated these and created version 7. Just in case any of you have further comments you would like to add please make them on this version (it makes my job a bit easier). All the best, Norman Susanna wrote: > Hi Norman and All, > > great job! > I suggest not to worry on this too much, as the editors will make such > suggestions/changes. > > Quick note to say that have just called Roy, Chief Editor, and we have > still few more days (Monday/Tuesday next week would be fine)!! > We/Ontology WG will produce a final version today, so these extra days > are key for us. > > Happy New Year! > Susanna > > Norman Morrison wrote: >> Dear All, >> >> I agree that the use of different fonts is not ideal. >> >> So far the options seem to be: >> >> 1) Matt's suggestion that we don't give 'sub-heading' status to S1 – >> Description of the …etc. and revert back to italics for optional items. >> 2) Oli's use of colour. I picked up an example copy of metabolomics at >> the metaboconf3 and it didn't have any colour in it. >> 3) Felicities use of asterisks'. >> >> I am happy to go with Matt's suggestion - alternatively we could leave >> it as it as and ask the formatting editor of the journal if they have >> any advice. I think at this stage it should still be clear to reviewers >> what we consider optional. >> >> Norman >> >> Matthew Davey wrote: >> >>> Dear all, >>> >>> I agree with Oli in that the times roman/arial fonts are difficult to >>> distinguish. >>> >>> I have lifted my comment from my previous edited document as one solution: >>> >>> ‘Still not sure about using different fonts to distinguish recommended >>> and optional information. Some websites offer html download instead of >>> pdf, in which case it will all be in the same font. One option is to >>> have the subheadings eg. S1 – Description of the … as non-italics as >>> they already standout due to the S1 etc code at the start and then >>> have the ‘optional information’ bits in italics.’ >>> >>> Cheers, >>> >>> Matt >>> >>> ------------------------------------------------------------------------ >>> >>> *From:* msi...@li... >>> [mailto:msi...@li...] >>> *On Behalf Of *Oliver Jones >>> *Sent:* 04 January 2007 10:17 >>> *To:* msi...@li... >>> *Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version 6 - >>> final comments by tomorrow please! >>> >>> Dear all, >>> >>> First off, a very happy new year to you all. I hope everybody enjoyed >>> the holidays? >>> >>> Right, now to business, swooping in at the very last minute as usualy >>> I have a few comments on different things. >>> >>> >>> *1) The paper* >>> >>> This looks excellent, thanks to everybody for the hard work. I hope it >>> is not too late but I'm made a few minor changes and comments to >>> version 6 (attached) which I think may be of use/interest. In response >>> to Normans question I think the following 'optional' form should be >>> left as it is. >>> >>> o Include details such as the type of housing, for example: Cage, >>> aquaria, continuous culture, seed bag or plant pot etc. >>> >>> I also agree with Mark and Norman that the merging of "description" >>> and "means" is a good idea for now. >>> >>> My only big worry is the use of the aerial font for optional only >>> parameters. I am not sure it shows up that well and I personally find >>> it a bit confusing especially if I convert the document to a pdf. >>> Unfortunately, I am at a loss at what else to suggest except maybe >>> different colours. However, that would probably be quite difficult so >>> I think we may just have to go with what we have. >>> >>> *2) Use case/real world examples/project description >>> >>> *There seems to be some confusion here. When I was formulating and >>> commenting on what I thought should be included in the requirements I >>> tried to draw on all my experience in Environmental Science and >>> metabolomics. Admittedly this may not be as extensive as some of the >>> people in the group but I still did not draw exclusively from just the >>> one project. To that end the described in my user case/real word >>> example/insert your description here was not retrofitted to the >>> standards but was worked through from the beginning and it took a fair >>> while to do. I think this is what Dalibor was trying to do as well. >>> (Speaking of Dalibor's examples I spotted a small mistake on page 5, >>> under section P5 – Description of acclimation of organism(s), in that >>> it still refers to the worms from my project. This will need to be >>> changed I think. There are also several references in the text but no >>> reference list at the end of the document). I think it is very useful >>> to have both user cases on the website so people cna see what are >>> proposing that they write. >>> >>> I do take Normans point about why user cases are useful though. >>> However, I send round something along those lines several weeks ago >>> that was reasonably comprehensive so perhaps we could just use that??? >>> However, if you want something more comprehensive I am afraid you will >>> have to give me a bit more time to prepare it (like an afternoon). >>> Either way please let me know ASAP. >>> >>> Cheers >>> >>> Oli >>> >>> >>> >>> >>> >>> Mark Viant wrote: >>> >>> Dear Norm et al >>> >>> I editted version 5, was about to send, and version 6 appeared! So >>> cut/paste my comments into latest version. All minor (except you cut a >>> reference). I am happy for this to be sent. Agree that merging >>> "description" and "means" is a good idea for now. >>> Mark >>> >>> >>> At 13:35 03/01/2007, Norman Morrison wrote: >>> >>> Dear All, >>> >>> Please find attached version 6(!) of the paper. I hoped to circulate >>> this yesterday but it took a bit longer than I had hoped. I think I >>> have now addressed all of the previous issues and have commented the >>> sections that I have changed. If you feel I have missed anything or >>> any of the issues have not been adequately addressed please let me >>> know :-) >>> >>> There was one issue that I think will require more thought. In the >>> process requirement groups there was a motion to merge 'Description' >>> and 'Means of' together. In my mind I believed that processes should >>> include a concise, 'free text' /description/, detailing the specific >>> process that has been applied or taken place, and that one should also >>> aim to provide a term(s) for the /means/ used (preferably from an >>> ontology or CV) in the application of the process. However, 'means' >>> seems to be a bit of a vague term, in that the examples we ourselves >>> provide, include descriptive terms that mix /actions/ (netted, >>> electrically stunned, etc) and /things/ (dry ice, formaldehyde). Given >>> this ambiguity, I think it might be best if we depricated 'means' for >>> the paper, but I think it will be worth revisiting in the next version >>> of the requirements. >>> >>> At the moment, I have kept the examples in the following 'optional' >>> form (see the paper): >>> >>> o Include details such as the type of housing, for example: Cage, >>> aquaria, continuous culture, seed bag or plant pot etc. >>> >>> ...or we could just get rid of them altogether. Thoughts? >>> >>> Hopefully there are not too many more changes to make at this late >>> stage, but I welcome your comments. Please can you get them back to me >>> by *12pm (GMT) tomorrow* at the latest, so that I can incorporate them >>> into the final version for submission. >>> >>> Thanks, >>> Norman >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys - and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________ >>> <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________> >>> >>> Msi-workgroups-env-bio-metadata mailing list >>> Msi...@li... >>> <mailto:Msi...@li...> >>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>> >>> >>> _______________________________________________ >>> Dr. Mark Viant >>> NERC Advanced Fellow in Metabolomics >>> School of Biosciences >>> The University of Birmingham >>> Birmingham, B15 2TT, U.K. >>> Phone +44-(0)121-414-2219 >>> FAX +44-(0)121-414-5925 >>> http://www.biosciences.bham.ac.uk/labs/viant/ >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> ------------------------------------------------------------------------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to share your >>> opinions on IT & business topics through brief surveys - and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> _______________________________________________ >>> Msi-workgroups-env-bio-metadata mailing list >>> Msi...@li... <mailto:Msi...@li...> >>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to share your >>> opinions on IT & business topics through brief surveys - and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Msi-workgroups-env-bio-metadata mailing list >>> Msi...@li... >>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata >>> >>> >> >> >> > > -- > Susanna-Assunta Sansone, PhD > > NET Project - Coordinator > > www.ebi.ac.uk/net-project > > The European Bioinformatics Institute email: sa...@eb... > EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 > Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > Cambridge CB10 1SD, UK room: A229 > > > -- Dr Norman Morrison NERC Omic Data Standards Coordinator Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 |
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From: Susanna <sa...@eb...> - 2007-01-04 13:55:22
|
Hi Norman and All, great job! I suggest not to worry on this too much, as the editors will make such=20 suggestions/changes. Quick note to say that have just called Roy, Chief Editor, and we have=20 still few more days (Monday/Tuesday next week would be fine)!! We/Ontology WG will produce a final version today, so these extra days=20 are key for us. Happy New Year! Susanna Norman Morrison wrote: >Dear All, > >I agree that the use of different fonts is not ideal. > >So far the options seem to be: > >1) Matt's suggestion that we don't give 'sub-heading' status to S1 =96=20 >Description of the =85etc. and revert back to italics for optional items. >2) Oli's use of colour. I picked up an example copy of metabolomics at=20 >the metaboconf3 and it didn't have any colour in it. >3) Felicities use of asterisks'. > >I am happy to go with Matt's suggestion - alternatively we could leave=20 >it as it as and ask the formatting editor of the journal if they have=20 >any advice. I think at this stage it should still be clear to reviewers=20 >what we consider optional. > >Norman > >Matthew Davey wrote: > =20 > >>Dear all, >> >>I agree with Oli in that the times roman/arial fonts are difficult to=20 >>distinguish. >> >>I have lifted my comment from my previous edited document as one soluti= on: >> >>=91Still not sure about using different fonts to distinguish recommende= d=20 >>and optional information. Some websites offer html download instead of=20 >>pdf, in which case it will all be in the same font. One option is to=20 >>have the subheadings eg. S1 =96 Description of the =85 as non-italics a= s=20 >>they already standout due to the S1 etc code at the start and then=20 >>have the =91optional information=92 bits in italics.=92 >> >>Cheers, >> >>Matt >> >>-----------------------------------------------------------------------= - >> >>*From:* msi...@li...=20 >>[mailto:msi...@li...]=20 >>*On Behalf Of *Oliver Jones >>*Sent:* 04 January 2007 10:17 >>*To:* msi...@li... >>*Subject:* Re: [Msi-workgroups-env-bio-metadata] Paper version 6 -=20 >>final comments by tomorrow please! >> >>Dear all, >> >>First off, a very happy new year to you all. I hope everybody enjoyed=20 >>the holidays? >> >>Right, now to business, swooping in at the very last minute as usualy=20 >>I have a few comments on different things. >> >> >>*1) The paper* >> >>This looks excellent, thanks to everybody for the hard work. I hope it=20 >>is not too late but I'm made a few minor changes and comments to=20 >>version 6 (attached) which I think may be of use/interest. In response=20 >>to Normans question I think the following 'optional' form should be=20 >>left as it is. >> >>o Include details such as the type of housing, for example: Cage,=20 >>aquaria, continuous culture, seed bag or plant pot etc. >> >>I also agree with Mark and Norman that the merging of "description"=20 >>and "means" is a good idea for now. >> >>My only big worry is the use of the aerial font for optional only=20 >>parameters. I am not sure it shows up that well and I personally find=20 >>it a bit confusing especially if I convert the document to a pdf.=20 >>Unfortunately, I am at a loss at what else to suggest except maybe=20 >>different colours. However, that would probably be quite difficult so=20 >>I think we may just have to go with what we have. >> >>*2) Use case/real world examples/project description >> >>*There seems to be some confusion here. When I was formulating and=20 >>commenting on what I thought should be included in the requirements I=20 >>tried to draw on all my experience in Environmental Science and=20 >>metabolomics. Admittedly this may not be as extensive as some of the=20 >>people in the group but I still did not draw exclusively from just the=20 >>one project. To that end the described in my user case/real word=20 >>example/insert your description here was not retrofitted to the=20 >>standards but was worked through from the beginning and it took a fair=20 >>while to do. I think this is what Dalibor was trying to do as well.=20 >>(Speaking of Dalibor's examples I spotted a small mistake on page 5,=20 >>under section P5 =96 Description of acclimation of organism(s), in that= =20 >>it still refers to the worms from my project. This will need to be=20 >>changed I think. There are also several references in the text but no=20 >>reference list at the end of the document). I think it is very useful=20 >>to have both user cases on the website so people cna see what are=20 >>proposing that they write. >> >>I do take Normans point about why user cases are useful though.=20 >>However, I send round something along those lines several weeks ago=20 >>that was reasonably comprehensive so perhaps we could just use that???=20 >>However, if you want something more comprehensive I am afraid you will=20 >>have to give me a bit more time to prepare it (like an afternoon).=20 >>Either way please let me know ASAP. >> >>Cheers >> >>Oli >> >> >>=20 >> >> >>Mark Viant wrote: >> >>Dear Norm et al >> >>I editted version 5, was about to send, and version 6 appeared! So=20 >>cut/paste my comments into latest version. All minor (except you cut a=20 >>reference). I am happy for this to be sent. Agree that merging=20 >>"description" and "means" is a good idea for now. >>Mark >> >> >>At 13:35 03/01/2007, Norman Morrison wrote: >> >>Dear All, >> >>Please find attached version 6(!) of the paper. I hoped to circulate=20 >>this yesterday but it took a bit longer than I had hoped. I think I=20 >>have now addressed all of the previous issues and have commented the=20 >>sections that I have changed. If you feel I have missed anything or=20 >>any of the issues have not been adequately addressed please let me=20 >>know :-) >> >>There was one issue that I think will require more thought. In the=20 >>process requirement groups there was a motion to merge 'Description'=20 >>and 'Means of' together. In my mind I believed that processes should=20 >>include a concise, 'free text' /description/, detailing the specific=20 >>process that has been applied or taken place, and that one should also=20 >>aim to provide a term(s) for the /means/ used (preferably from an=20 >>ontology or CV) in the application of the process. However, 'means'=20 >>seems to be a bit of a vague term, in that the examples we ourselves=20 >>provide, include descriptive terms that mix /actions/ (netted,=20 >>electrically stunned, etc) and /things/ (dry ice, formaldehyde). Given=20 >>this ambiguity, I think it might be best if we depricated 'means' for=20 >>the paper, but I think it will be worth revisiting in the next version=20 >>of the requirements. >> >>At the moment, I have kept the examples in the following 'optional'=20 >>form (see the paper): >> >>o Include details such as the type of housing, for example: Cage,=20 >>aquaria, continuous culture, seed bag or plant pot etc. >> >>...or we could just get rid of them altogether. Thoughts? >> >>Hopefully there are not too many more changes to make at this late=20 >>stage, but I welcome your comments. Please can you get them back to me=20 >>by *12pm (GMT) tomorrow* at the latest, so that I can incorporate them=20 >>into the final version for submission. >> >>Thanks, >>Norman >> >> >> >> >> >> >> >>-----------------------------------------------------------------------= -- >>Take Surveys. Earn Cash. Influence the Future of IT >>Join SourceForge.net's Techsay panel and you'll get the chance to=20 >>share your >>opinions on IT & business topics through brief surveys - and earn cash >>http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV_______________________________________________=20 >><http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV_______________________________________________>=20 >> >>Msi-workgroups-env-bio-metadata mailing list >>Msi...@li...=20 >><mailto:Msi...@li...> >>https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-met= adata=20 >> >> >>_______________________________________________ >>Dr. Mark Viant >>NERC Advanced Fellow in Metabolomics >>School of Biosciences >>The University of Birmingham >>Birmingham, B15 2TT, U.K. >>Phone +44-(0)121-414-2219 >>FAX +44-(0)121-414-5925 >>http://www.biosciences.bham.ac.uk/labs/viant/ >> >>=20 >> >> >>-----------------------------------------------------------------------= - >> >> >>=20 >>-----------------------------------------------------------------------= -- >>Take Surveys. Earn Cash. Influence the Future of IT >>Join SourceForge.net's Techsay panel and you'll get the chance to share= your >>opinions on IT & business topics through brief surveys - and earn cash >>http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV <http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforg= e&CID=3DDEVDEV> >>=20 >> >> >>-----------------------------------------------------------------------= - >> >> >>=20 >>_______________________________________________ >>Msi-workgroups-env-bio-metadata mailing list >>Msi...@li... <mailto:Msi-workg= rou...@li...> >>https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-met= adata >> =20 >>-----------------------------------------------------------------------= - >> >>-----------------------------------------------------------------------= -- >>Take Surveys. Earn Cash. Influence the Future of IT >>Join SourceForge.net's Techsay panel and you'll get the chance to share= your >>opinions on IT & business topics through brief surveys - and earn cash >>http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV >>-----------------------------------------------------------------------= - >> >>_______________________________________________ >>Msi-workgroups-env-bio-metadata mailing list >>Msi...@li... >>https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-met= adata >> =20 >> =20 >> > > > =20 > --=20 Susanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project =09 The European Bioinformatics Institute email: sa...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK room: A229 =20 =20 |
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From: Mark V. <m....@bh...> - 2007-01-04 13:50:03
|
Oli - is this it? mark At 12:14 04/01/2007, Oliver Jones wrote: >Dear all, > >Sorry to be a pain but I am hoping somebody might be able to save me >some time. Way back when we started working on these standards I sent >round what I think we have now agreed to define as a brief user case. >Unfortunately, I seem to have saved over this with my real world >example. If anybody has my original file in the depths of their inbox >would it be possible for you to send it to me please? I can then update >and expand it to match the others and send it back out for inclusion in >the paper and the website. > >Thanks > >Oli > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Msi-workgroups-env-bio-metadata mailing list >Msi...@li... >https://lists.sourceforge.net/lists/listinfo/msi-workgroups-env-bio-metadata |
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From: Oliver J. <oa...@mo...> - 2007-01-04 12:27:02
|
Dear all, Sorry, me again but just to let you know you can ignore my last message now. Matt Davey have very kindly forwarded the file on to me. Cheers Oli |
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From: Oliver J. <oa...@mo...> - 2007-01-04 12:15:06
|
Dear all, Sorry to be a pain but I am hoping somebody might be able to save me some time. Way back when we started working on these standards I sent round what I think we have now agreed to define as a brief user case. Unfortunately, I seem to have saved over this with my real world example. If anybody has my original file in the depths of their inbox would it be possible for you to send it to me please? I can then update and expand it to match the others and send it back out for inclusion in the paper and the website. Thanks Oli |
5 messages has been excluded from this view by a project administrator.
