You can subscribe to this list here.
2006 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(1) |
Jun
(10) |
Jul
(17) |
Aug
(8) |
Sep
(47) |
Oct
(34) |
Nov
(3) |
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2007 |
Jan
(19) |
Feb
(13) |
Mar
(5) |
Apr
(5) |
May
(7) |
Jun
(7) |
Jul
|
Aug
|
Sep
|
Oct
(6) |
Nov
(5) |
Dec
(1) |
2008 |
Jan
|
Feb
(20) |
Mar
(8) |
Apr
(5) |
May
(3) |
Jun
(3) |
Jul
(4) |
Aug
|
Sep
(1) |
Oct
(22) |
Nov
(12) |
Dec
(3) |
2009 |
Jan
(4) |
Feb
|
Mar
(6) |
Apr
(3) |
May
(1) |
Jun
(3) |
Jul
(2) |
Aug
(18) |
Sep
(3) |
Oct
(12) |
Nov
(2) |
Dec
|
2010 |
Jan
|
Feb
(3) |
Mar
(2) |
Apr
(5) |
May
(11) |
Jun
|
Jul
(15) |
Aug
(53) |
Sep
(4) |
Oct
(15) |
Nov
(17) |
Dec
(2) |
2011 |
Jan
(22) |
Feb
(43) |
Mar
(20) |
Apr
(9) |
May
(20) |
Jun
(75) |
Jul
(87) |
Aug
(7) |
Sep
(8) |
Oct
(16) |
Nov
(11) |
Dec
(12) |
2012 |
Jan
(4) |
Feb
(6) |
Mar
|
Apr
|
May
|
Jun
|
Jul
(1) |
Aug
|
Sep
|
Oct
(10) |
Nov
(9) |
Dec
|
2013 |
Jan
|
Feb
(12) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(5) |
Nov
(4) |
Dec
|
2014 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(3) |
Sep
(2) |
Oct
(3) |
Nov
|
Dec
|
2015 |
Jan
|
Feb
|
Mar
(3) |
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
2016 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
From: Chris M. <cjm...@lb...> - 2012-10-30 15:42:24
|
Hi Erick I recommend you use property_value tag and request the properties below from IAO. The modification date would be an xsd:date. Given that there may be multiple modification I suggest requesting "last modification date", or modeling each modification as a separate entity (outside what can be done easily in obo-format). It's not clear how this would be used - at the moment neither Protege not OE tracks this (though it may be useful for them to do so) On Tue, Oct 30, 2012 at 12:42 AM, Erick Antezana <eri...@gm...> wrote: > Hi, > > I would like to request the addition of two new tags: modified_by and > modification_date (unless there is a better way/practice to keep track > of atomic/term modifications...) > > modified_by: erick > modification_date: 2012-10-30T08:40:22Z > > I recall those tags were at some point present in TO > (https://groups.google.com/forum/?fromgroups=#!topic/obo-format/de0vV-2KrxQ)... > > cheers, > Erick > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
From: Erick A. <eri...@gm...> - 2012-10-30 07:42:37
|
Hi, I would like to request the addition of two new tags: modified_by and modification_date (unless there is a better way/practice to keep track of atomic/term modifications...) modified_by: erick modification_date: 2012-10-30T08:40:22Z I recall those tags were at some point present in TO (https://groups.google.com/forum/?fromgroups=#!topic/obo-format/de0vV-2KrxQ)... cheers, Erick |
From: Mike C. <ch...@st...> - 2012-10-19 17:35:45
|
Dear Colleagues, The International Biocuration Conference is a unique event for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For the 6th International Biocuration Conference in Cambridge UK you are invited to submit your work for publication. This call for papers is done in collaboration with DATABASE: The Journal of Biological Databases and Curation. The DATABASE journal will publish an online Virtual Issue of the accepted papers. This is a great occasion to enhance the recognition of your work and of our profession by the greater biological research communities. This year there are five topic sessions from which submitters are invited to select: 1. Community annotation 2. Functional annotation, tools and pipelines 3. Data mining and automated prediction 4. Ontologies and Standards 5. Data integration: Interactions, pathways and networks An additional session, “Lightning talks/hot topics”, will include presentations outside the above topics. The manuscript review process will be expedited for these papers and we will thus need to be firm on the submission deadline: - Submission deadline: November 30, 2012 - First decisions: January 7, 2013 - Deadline for revisions: January 28, 2013 - Final decisions: February 18, 2013 - Conference: April 7-10, 2013 Authors wishing to submit to DATABASE for the 2013 Biocuration Virtual issue should go to the DATABASE home page (http://database.oxfordjournals.org/) and click on the "submit now" after having read the "Instructions to Authors". Authors should CLEARLY state that they are submitting this manuscript for consideration for the Biocuration 2013 conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting's proceedings. In addition, in the database submission form, they should also select "Biocuration Conference Paper" as a manuscript type. We look forward to your participation at Biocuration 2013 the 6th International Biocuration Conference. To be considered for a Biocuration 2013 presentation you MUST register and SUBMIT an abstract for the meeting <http://www.ebi.ac.uk/biocuration2013/>. On the abstract submission form, note that you will submit a manuscript for consideration by DATABASE for the Biocuration 2013 Virtual Issue. The proceedings of the 2012 meeting, the Biocuration 2012 Virtual Issue, are online <http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html> Kind regards, -Biocuration 2013 Organizing Committee |
From: Chris M. <cjm...@lb...> - 2012-07-17 00:43:54
|
I propose a minor addition the current draft that will allow us to capture a range of ontology metadata. Should have been added before, sorry about the oversight http://code.google.com/p/oboformat/issues/detail?id=71 post on the tracker if you have objections |
From: Chris M. <cjm...@lb...> - 2012-02-15 16:12:45
|
Hi Savs, It' still not clear what you mean by store xml data - do you want to just encode a big blob of xml - or do you want to take what is being modeled in that xml and model it directly in obo? Regarding validation - you can syntatically validate your obo-format file using the reference obo2owl translator (http://oboformat.org) For semantic validation, every obo file is an owl ontology, you can use any owl reasoner. If you've found bugs in the spec or implementation can you post them to the tracker (or send the patches to me) thanks! On Feb 15, 2012, at 5:30 AM, Savaş TAKAN wrote: > I want to use obo for storage purpose ( storing xml data). for doing this, I think that instance is suitable for this and obo have such as facility ( http://oboformat.googlecode.com/svn/branches/2011-11-29/doc/obo-syntax.html ). > > I want to use obo because of readability (turtle and rdf/xml are not good readable.) > I changed obo format library for creating instance by BNF and also solved xref problem ( i think it is bug). > > but obo format don't have validation, reasoner. I need to solve these. do you have any suggestion ? > > > Savaş TAKAN > Research Assistant at İzmir Institute of Technology > Computer Engineer > > > > > 2012/2/14 Chris Mungall <cjm...@lb...> > Hi Savaş > > I'm not sure I understand the question. What do you mean by add xml to psi-ms.obo? > > On Feb 4, 2012, at 8:51 AM, Savas wrote: > > > Dear Obo-discuss, > > > > I am msc student at iyte. in my thesis, I need add xml data ( > > http://proteowizard.sourceforge.net/example_data/tiny.pwiz.1.1.mzML ) > > to psi-ms.obo (http://psidev.sourceforge.net/mi/psi-mi.obo) by obo > > format library > > > > I don't find way how to add xml data. if you help me, I am very happy. > > > > Note : I attached needed files. > > > > regards, > > > > Savaş TAKAN > > Research Assistant at İzmir Institute of Technology > > Computer Engineer > > > > ------------------------------------------------------------------------------ > > Virtualization & Cloud Management Using Capacity Planning > > Cloud computing makes use of virtualization - but cloud computing > > also focuses on allowing computing to be delivered as a service. > > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > > _______________________________________________ > > Obo-format mailing list > > Obo...@li... > > https://lists.sourceforge.net/lists/listinfo/obo-format > > |
From: Savaş T. <sav...@gm...> - 2012-02-15 13:31:11
|
I want to use obo for storage purpose ( storing xml data). for doing this, I think that instance is suitable for this and obo have such as facility ( http://oboformat.googlecode.com/svn/branches/2011-11-29/doc/obo-syntax.html ). I want to use obo because of readability (turtle and rdf/xml are not good readable.) I changed obo format library for creating instance by BNF and also solved xref problem ( i think it is bug). but obo format don't have validation, reasoner. I need to solve these. do you have any suggestion ? Savaş TAKAN Research Assistant at İzmir Institute of Technology Computer Engineer 2012/2/14 Chris Mungall <cjm...@lb...> > Hi Savaş > > I'm not sure I understand the question. What do you mean by add xml to > psi-ms.obo? > > On Feb 4, 2012, at 8:51 AM, Savas wrote: > > > Dear Obo-discuss, > > > > I am msc student at iyte. in my thesis, I need add xml data ( > > http://proteowizard.sourceforge.net/example_data/tiny.pwiz.1.1.mzML ) > > to psi-ms.obo (http://psidev.sourceforge.net/mi/psi-mi.obo) by obo > > format library > > > > I don't find way how to add xml data. if you help me, I am very happy. > > > > Note : I attached needed files. > > > > regards, > > > > Savaş TAKAN > > Research Assistant at İzmir Institute of Technology > > Computer Engineer > > > > > ------------------------------------------------------------------------------ > > Virtualization & Cloud Management Using Capacity Planning > > Cloud computing makes use of virtualization - but cloud computing > > also focuses on allowing computing to be delivered as a service. > > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > > _______________________________________________ > > Obo-format mailing list > > Obo...@li... > > https://lists.sourceforge.net/lists/listinfo/obo-format > > |
From: Chris M. <cjm...@lb...> - 2012-02-14 23:39:39
|
http://purl.obolibrary.org/obo/oboformat/spec.html For the syntax see #3.5, and the mapping to OWL, see #5.5 However, tools built around obo-format are generally instance-ignorant. There's not really any use case for instances in obo-format, they're there for historic purposes. You might want to consider rdf/owl On Feb 11, 2012, at 6:25 AM, Savas wrote: > how can add instance to obo ontology. I think obo format library > doesn't add instance, is it true ? > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
From: Chris M. <cjm...@lb...> - 2012-02-13 22:44:08
|
Hi Savaş I'm not sure I understand the question. What do you mean by add xml to psi-ms.obo? On Feb 4, 2012, at 8:51 AM, Savas wrote: > Dear Obo-discuss, > > I am msc student at iyte. in my thesis, I need add xml data ( > http://proteowizard.sourceforge.net/example_data/tiny.pwiz.1.1.mzML ) > to psi-ms.obo (http://psidev.sourceforge.net/mi/psi-mi.obo) by obo > format library > > I don't find way how to add xml data. if you help me, I am very happy. > > Note : I attached needed files. > > regards, > > Savaş TAKAN > Research Assistant at İzmir Institute of Technology > Computer Engineer > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
From: Savas <sav...@gm...> - 2012-02-11 14:25:40
|
how can add instance to obo ontology. I think obo format library doesn't add instance, is it true ? |
From: Savas <sav...@gm...> - 2012-02-04 16:52:02
|
Dear Obo-discuss, I am msc student at iyte. in my thesis, I need add xml data ( http://proteowizard.sourceforge.net/example_data/tiny.pwiz.1.1.mzML ) to psi-ms.obo (http://psidev.sourceforge.net/mi/psi-mi.obo) by obo format library I don't find way how to add xml data. if you help me, I am very happy. Note : I attached needed files. regards, Savaş TAKAN Research Assistant at İzmir Institute of Technology Computer Engineer |
From: Melanie C. <mco...@gm...> - 2012-01-23 19:36:08
|
Hi, I am wondering if by review you mean some sort of endorsement, or if you just mean somebody who contributed to the term? In the first case, you would want something like "term validated by" (but maybe it will be too granular to manage those at the term level? When does a review becomes invalid/superseded?) and in the latter we could maybe just add a curator note "synonym added on 2009-04-28T10:22:40Z by John Doe"? Cheers, Melanie On 2012-01-12, at 9:58 AM, Chris Mungall wrote: > > I would suggest first of all getting the property into IAO ontology-metadata and then we can decide whether to add a new tag or use a generic property_value tag. > > For a generic property_value tag and for the OWL translation the second is easier as it's doesn't involve multiple values for the same tag, but is obviously more limited as you can't have >1 review. > > The requirements for reviews are likely to be quite varied. > > On Jan 12, 2012, at 6:05 AM, Erick Antezana wrote: > >> Hi David, >> >> I fully support your request of having a means to credit ontology >> contributors. Do you have an example of the usage of such a tag? >> >> reviewed_by: john_doe 2009-04-28T10:22:40Z >> >> or >> >> reviewed_by: "John Doe" [2009-04-28T10:22:40Z] >> >> or >> >> reviewed_by: john_doe >> revision_date: 2009-04-28T10:22:40Z >> >> or >> >> reviwed_by: john_doe {2009-04-28T10:22:40Z} ! DNA binding RNA >> polymerase II transcription factor activity corrected >> >> What about the possible duplication of data while also using the extant tags: >> >> created_by: jdoe >> creation_date: 2009-04-28T10:22:40Z >> >> What if there are several "reviewers"? >> >> Does "any type" of contribution would make somebody a 'reviewer'? >> (e.g. refining a definition, providing a synonym, suggesting to fix a >> typo, fixing a relationship linking a given term, ...) >> >> cheers, >> Erick >> >> On 12 January 2012 14:22, David Osumi-Sutherland <dj...@ge...> wrote: >>> Hi there, >>> >>> We're exploring ways to give credit to those who've provided expert feedback to us on the accuracy of definitions and relationships for specific sets of terms in our ontology. One way to do this would be to flag reviewed terms using a new tag-value pair in OBO. For this purpose, I'd like to request a reviewed_by tag in OBO (1.4?). We will, of course, need a corresponding OWL annotation property. >>> >>> It would be useful to record two values - in addition to a name, a date or ontology version number for the review would make it clear what version of a term a reviewer has signed off on. In OWL the version info could be an annotation of an annotation. In OBO this could be in a trailing modifier (http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4). >>> >>> Does this seem reasonable? >>> >>> Cheers, >>> David >>> >>> >>> David Osumi-Sutherland, PhD >>> Ontologist >>> FlyBase / Virtual Fly Brain >>> Department of Genetics, >>> University of Cambridge, >>> Downing Street, >>> Cambridge, CB2 3EH, UK >>> Tel: +44 (0)1223 333 963 >>> Fax: +44 (0)1223 766 732 >>> http://www.virtualflybrain.org >>> >>> >>> ------------------------------------------------------------------------------ >>> RSA(R) Conference 2012 >>> Mar 27 - Feb 2 >>> Save $400 by Jan. 27 >>> Register now! >>> http://p.sf.net/sfu/rsa-sfdev2dev2 >>> _______________________________________________ >>> Obo-format mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-format >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Mar 27 - Feb 2 >> Save $400 by Jan. 27 >> Register now! >> http://p.sf.net/sfu/rsa-sfdev2dev2 >> _______________________________________________ >> Obo-format mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-format > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format --- Mélanie Courtot MSFHR/PCIRN trainee, TFL- BCCRC 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada |
From: Chris M. <cjm...@lb...> - 2012-01-12 17:59:07
|
I would suggest first of all getting the property into IAO ontology-metadata and then we can decide whether to add a new tag or use a generic property_value tag. For a generic property_value tag and for the OWL translation the second is easier as it's doesn't involve multiple values for the same tag, but is obviously more limited as you can't have >1 review. The requirements for reviews are likely to be quite varied. On Jan 12, 2012, at 6:05 AM, Erick Antezana wrote: > Hi David, > > I fully support your request of having a means to credit ontology > contributors. Do you have an example of the usage of such a tag? > > reviewed_by: john_doe 2009-04-28T10:22:40Z > > or > > reviewed_by: "John Doe" [2009-04-28T10:22:40Z] > > or > > reviewed_by: john_doe > revision_date: 2009-04-28T10:22:40Z > > or > > reviwed_by: john_doe {2009-04-28T10:22:40Z} ! DNA binding RNA > polymerase II transcription factor activity corrected > > What about the possible duplication of data while also using the extant tags: > > created_by: jdoe > creation_date: 2009-04-28T10:22:40Z > > What if there are several "reviewers"? > > Does "any type" of contribution would make somebody a 'reviewer'? > (e.g. refining a definition, providing a synonym, suggesting to fix a > typo, fixing a relationship linking a given term, ...) > > cheers, > Erick > > On 12 January 2012 14:22, David Osumi-Sutherland <dj...@ge...> wrote: >> Hi there, >> >> We're exploring ways to give credit to those who've provided expert feedback to us on the accuracy of definitions and relationships for specific sets of terms in our ontology. One way to do this would be to flag reviewed terms using a new tag-value pair in OBO. For this purpose, I'd like to request a reviewed_by tag in OBO (1.4?). We will, of course, need a corresponding OWL annotation property. >> >> It would be useful to record two values - in addition to a name, a date or ontology version number for the review would make it clear what version of a term a reviewer has signed off on. In OWL the version info could be an annotation of an annotation. In OBO this could be in a trailing modifier (http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4). >> >> Does this seem reasonable? >> >> Cheers, >> David >> >> >> David Osumi-Sutherland, PhD >> Ontologist >> FlyBase / Virtual Fly Brain >> Department of Genetics, >> University of Cambridge, >> Downing Street, >> Cambridge, CB2 3EH, UK >> Tel: +44 (0)1223 333 963 >> Fax: +44 (0)1223 766 732 >> http://www.virtualflybrain.org >> >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Mar 27 - Feb 2 >> Save $400 by Jan. 27 >> Register now! >> http://p.sf.net/sfu/rsa-sfdev2dev2 >> _______________________________________________ >> Obo-format mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-format > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
From: Erick A. <eri...@gm...> - 2012-01-12 14:06:01
|
Hi David, I fully support your request of having a means to credit ontology contributors. Do you have an example of the usage of such a tag? reviewed_by: john_doe 2009-04-28T10:22:40Z or reviewed_by: "John Doe" [2009-04-28T10:22:40Z] or reviewed_by: john_doe revision_date: 2009-04-28T10:22:40Z or reviwed_by: john_doe {2009-04-28T10:22:40Z} ! DNA binding RNA polymerase II transcription factor activity corrected What about the possible duplication of data while also using the extant tags: created_by: jdoe creation_date: 2009-04-28T10:22:40Z What if there are several "reviewers"? Does "any type" of contribution would make somebody a 'reviewer'? (e.g. refining a definition, providing a synonym, suggesting to fix a typo, fixing a relationship linking a given term, ...) cheers, Erick On 12 January 2012 14:22, David Osumi-Sutherland <dj...@ge...> wrote: > Hi there, > > We're exploring ways to give credit to those who've provided expert feedback to us on the accuracy of definitions and relationships for specific sets of terms in our ontology. One way to do this would be to flag reviewed terms using a new tag-value pair in OBO. For this purpose, I'd like to request a reviewed_by tag in OBO (1.4?). We will, of course, need a corresponding OWL annotation property. > > It would be useful to record two values - in addition to a name, a date or ontology version number for the review would make it clear what version of a term a reviewer has signed off on. In OWL the version info could be an annotation of an annotation. In OBO this could be in a trailing modifier (http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4). > > Does this seem reasonable? > > Cheers, > David > > > David Osumi-Sutherland, PhD > Ontologist > FlyBase / Virtual Fly Brain > Department of Genetics, > University of Cambridge, > Downing Street, > Cambridge, CB2 3EH, UK > Tel: +44 (0)1223 333 963 > Fax: +44 (0)1223 766 732 > http://www.virtualflybrain.org > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
From: David Osumi-S. <dj...@ge...> - 2012-01-12 13:22:19
|
Hi there, We're exploring ways to give credit to those who've provided expert feedback to us on the accuracy of definitions and relationships for specific sets of terms in our ontology. One way to do this would be to flag reviewed terms using a new tag-value pair in OBO. For this purpose, I'd like to request a reviewed_by tag in OBO (1.4?). We will, of course, need a corresponding OWL annotation property. It would be useful to record two values - in addition to a name, a date or ontology version number for the review would make it clear what version of a term a reviewer has signed off on. In OWL the version info could be an annotation of an annotation. In OBO this could be in a trailing modifier (http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4). Does this seem reasonable? Cheers, David David Osumi-Sutherland, PhD Ontologist FlyBase / Virtual Fly Brain Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK Tel: +44 (0)1223 333 963 Fax: +44 (0)1223 766 732 http://www.virtualflybrain.org |
From: Chris M. <cjm...@lb...> - 2011-12-14 23:03:34
|
Just a heads up for any software developers using the oboformat.jar or the oboformat source: We've organized the directory structure into a standard maven layout. The jar is now in the bin/ directory, and is called "oboformat-all.jar", and this now contains all dependencies (owlapi, etc). You can also get the core jar from our Maven repository - the current release is 0.5.0: http://code.berkeleybop.org/maven/repository/org/bbop/oboformat/0.5.0/ ** If you run obolib-obo2owl or obolib-owl2obo on the command line this shouldn't affect you ** |
From: Chris M. <cjm...@lb...> - 2011-12-14 20:10:31
|
Subscribers to this list will no longer be bothered by the emails auto-sent from the googlecode issues tracker. If you want to keep receiving these, sign up here: https://groups.google.com/group/oboformat-issue-tracker |
From: <obo...@go...> - 2011-12-14 19:00:44
|
Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 62 by mcour...@gmail.com: Specification scetion 2.3 http://code.google.com/p/oboformat/issues/detail?id=62 The notation ws* is introduced but not defined. As section 2.1 table 1 says zero or more will be noted with curly braces, it would probably make more sense to use {ws} instead of ws*. SImilarly for nl* in the section 2.2 above. I am not sure how to define a Qualifier. Maybe something along the lines of "A Qualifier expresses a relationship between the object of the annotation and a well-defined semantic entity." from http://code.google.com/p/annotation-ontology/wiki/Qualifiers Maybe having an example of OBO file with different elements examplified and named would help? Maybe as an annex to the spec? |
From: <obo...@go...> - 2011-12-14 17:06:18
|
Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 61 by mcour...@gmail.com: Specification - section 2.2 http://code.google.com/p/oboformat/issues/detail?id=61 I find it would be useful to add a bit more explanation to this section. 1. define Letter and Char. I suspect <Letter> ::= a|b|c|d|e|f|g|h|i|j|k|l|m|n|o|p|q|r|s|t|u|v|w|x|y|z |A|B|C|D|E|F|G|H|I|J|K|L|M|N|O|P|Q|R|S|T|U|V|W|X|Y|Z <digit> ::= 1|2|3|4|5|6|7|8|9|0 <Char> ::= <Letter> | <digit> | (I don't know the appropriate notation to encompass NewLineChar etc) Note that the usual use of <char> I found on the web was for <letter> | <digit> 2. expand on nl* and nl+ nl* ::= {nl} means 0 or more occurrences of nl nl+ ::= nl {nl} means at least 1 occurrence followed by 0 or more (note that I replaced {ws NewLineChar} by {nl} for nl+ to be consistent with nl* 3. OBOChar If I understand that one it is meant to provide a way to escape things? Based on the notation, an example of OBOChar would be (adding quotes to limit each example) "\A" or "\ 1 &" Would it be possible to add a few words on what is OBOChar and how it is to be used to make it clearer? |
From: David Osumi-S. <dj...@ge...> - 2011-12-14 15:28:09
|
On 14 Dec 2011, at 14/Dec/2011 14:53:13, Alan Ruttenberg wrote: > On Wed, Dec 14, 2011 at 8:17 AM, Melissa Haendel <ha...@oh...> wrote: >> Hi David, >> not sure if this is what you are looking for, but we've been able to get a >> MeSH taxonomy out of NCBO for use as a reference taxonomy in eagle-i using >> their view extractor tool: >> http://www.bioontology.org/wiki/index.php/View_Extraction >> >> The classes look like this: >> <!-- http://purl.bioontology.org/ontology/MSH/D000008 --> >> >> <owl:Class rdf:about="http://purl.bioontology.org/ontology/MSH/D000008"> >> <rdfs:label>Abdominal Neoplasms</rdfs:label> >> <rdfs:subClassOf >> rdf:resource="http://purl.bioontology.org/ontology/MSH/D009371"/> >> </owl:Class> > > > The MeSH terms are not related by subClassOf, they constitute a > terminology and should be related by the skos broader* etc > relationships. > Moreover the MeSH version on bioportal seems to be an extraction from > UMLS rather that primary source. As such the relation names as > displayed are ... obscure. > Only a careful review would let one assess whether some of the > relations warrant being subclass relations. > If David is only using the publication terms then it shouldn't matter to him. > > We have a neurocommons MeSH version that is based on an earlier skos > version, but also creates terms for each term/qualifier pair (since > these tend to have different meanings. I would recommend that or > another version that builds upon it be used. See > http://neurocommons.org/page/Bundles/mesh/mesh-skos OK. Given that I need something now, this looks like a good way to go for the semantics. I'm clear on how to do this in OWL In Manchester syntax: <http://purl.obolibrary.org/obo/FBcv_0000207> equivalentTo <http://purl.org/commons/record/mesh/D016422> And we can now express equivalence in OBO. However, it's not clear to me how we deal with the full URL for the MeSH term in OBO though - a question for Chris Mungall I think. That deals with the semantics, but given that these commons purls don't resolve to anything useful, I think it's also worth having an xref in place that expands to something that does. It's probably sufficient for this to be linked to the definition. This could be the bioportal purl, or a direct link to the MeSH site. I'd prefer the latter, but it seems like only the way we get this is with year specific GO.xrf_abbs entry. Cheers, David > > A lasting rendering of MeSH suitable for use within the OBO Foundry, > would, I think, be one based on IAO, as MeSH is an indexing resource, > rather than a referring ontology. It would take care with qualified > terms, and have some theory of how to manage reference to terms in > specific yearly versions. My recommendation for simple xref, > would be (in this order) > > - A version of MeSH based on IAO taking into account the issues noted > - A version of MeSH based on the Neurocommons version, which is > SKOS-based, takes care with qualifiers, and is built direct from MeSH > source, but not the versioning issues. > - A direct link to the MeSH web space. > - The current bioportal version (this falls under the line of recommended) > > -Alan > >> >> Note there were some errors in the ID generation when we did this a while >> back, so check the output URIs carefully if you go this route. >> >> No year though. Could probably add that. I think it would be great if we/OBO >> could agree on a standard here though, there are numerous occasions to >> reference MeSH for reasonable purposes. >> >> Cheers, >> Melissa >> >> >> On Dec 14, 2011, at 7:46 AM, David Osumi-Sutherland wrote: >> >> Hi all, >> >> We're in the process of mapping FlyBase publication type terms to MeSH. >> This makes us consistent with PubMed - the main source of our biblio data. >> >> >> Ideally I'd like to be able to make EquivalentClass links, but presumably >> I'd need an up-to-date version of MeSH in OBO or OWL for that to be viable ? >> If so, does anyone know if there is one available? >> >> In the absence of this, I've been looking at using the OBO xref mechanism >> (which is also useful for attributing definitions.) >> >> Unfortunately, xrefs to MeSH are somewhat problematic. Here's the >> GO.xrf_abbs entry: >> >> abbreviation: MeSH >> database: Medical Subject Headings >> object: MeSH heading >> example_id: MeSH:mitosis >> generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html >> url_syntax: >> http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id] >> url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis >> >> Note the year embedded in the URL. It seems that the name/year combination >> gives a stable reference. But to use this, we would need a new MeSH xref >> abbreviation for each year. There's also a further wrinkle to this: >> >> "Cell Transformation, Neoplastic" >> >> >> http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic >> >> This feels unsatisfactory, but I'm not sure there is any other good option. >> >> MeSH terms have unique IDs, but as far as I can gather, there is no way to >> use these to roll a URL (although you can query them from here >> http://www.nlm.nih.gov/mesh/2010/mesh_browser/MBrowser.html). >> >> Tree node IDs have been used by GO curators, e.g.: >> >> id: GO:0006927 >> name: transformed cell apoptosis >> namespace: biological_process >> def: "The process of apoptosis in transformed cells, cells that have >> undergone changes manifested by escape from control mechanisms, increased >> growth potential, alterations in the cell surface, karyotypic abnormalities, >> morphological and biochemical deviations from the norm." [GOC:jl, >> MeSH:C04.697.152] >> >> These can be used to roll URLs in combination with a year and term name: >> >> http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic&field=entry#TreeC04.697.152 >> >> i.e.- they appear to only be useful for specifying which, of multiple >> possible tree nodes for a term to display on linking. >> >> So - can we have year specific xrefs for MeSH in order to get reliable >> expansions? It has the advantage of recording version information for free. >> Or does anyone have a better suggestion? >> >> Cheers, >> >> David >> >> >> >> David Osumi-Sutherland, PhD >> Ontologist >> FlyBase / Virtual Fly Brain >> Department of Genetics, >> University of Cambridge, >> Downing Street, >> Cambridge, CB2 3EH, UK >> Tel: +44 (0)1223 333 963 >> Fax: +44 (0)1223 766 732 >> http://www.virtualflybrain.org >> >> >> ------------------------------------------------------------------------------ >> Cloud Computing - Latest Buzzword or a Glimpse of the Future? >> This paper surveys cloud computing today: What are the benefits? >> Why are businesses embracing it? What are its payoffs and pitfalls? >> http://www.accelacomm.com/jaw/sdnl/114/51425149/ >> _______________________________________________ >> Obo-format mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-format >> >> >> Dr. Melissa Haendel >> >> eagle-i Networking Research Resources >> OHSU Library http://www.ohsu.edu/library/ >> Department of Medical Informatics and Epidemiology >> Oregon Health & Science University >> ha...@oh... >> skype: melissa.haendel >> 503-407-5970 >> >> >> >> ------------------------------------------------------------------------------ >> Cloud Computing - Latest Buzzword or a Glimpse of the Future? >> This paper surveys cloud computing today: What are the benefits? >> Why are businesses embracing it? What are its payoffs and pitfalls? >> http://www.accelacomm.com/jaw/sdnl/114/51425149/ >> _______________________________________________ >> Obo-format mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-format >> > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss David Osumi-Sutherland, PhD Ontologist FlyBase / Virtual Fly Brain Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK Tel: +44 (0)1223 333 963 Fax: +44 (0)1223 766 732 http://www.virtualflybrain.org |
From: Alan R. <ala...@gm...> - 2011-12-14 14:53:50
|
On Wed, Dec 14, 2011 at 8:17 AM, Melissa Haendel <ha...@oh...> wrote: > Hi David, > not sure if this is what you are looking for, but we've been able to get a > MeSH taxonomy out of NCBO for use as a reference taxonomy in eagle-i using > their view extractor tool: > http://www.bioontology.org/wiki/index.php/View_Extraction > > The classes look like this: > <!-- http://purl.bioontology.org/ontology/MSH/D000008 --> > > <owl:Class rdf:about="http://purl.bioontology.org/ontology/MSH/D000008"> > <rdfs:label>Abdominal Neoplasms</rdfs:label> > <rdfs:subClassOf > rdf:resource="http://purl.bioontology.org/ontology/MSH/D009371"/> > </owl:Class> The MeSH terms are not related by subClassOf, they constitute a terminology and should be related by the skos broader* etc relationships. Moreover the MeSH version on bioportal seems to be an extraction from UMLS rather that primary source. As such the relation names as displayed are ... obscure. Only a careful review would let one assess whether some of the relations warrant being subclass relations. If David is only using the publication terms then it shouldn't matter to him. We have a neurocommons MeSH version that is based on an earlier skos version, but also creates terms for each term/qualifier pair (since these tend to have different meanings. I would recommend that or another version that builds upon it be used. See http://neurocommons.org/page/Bundles/mesh/mesh-skos A lasting rendering of MeSH suitable for use within the OBO Foundry, would, I think, be one based on IAO, as MeSH is an indexing resource, rather than a referring ontology. It would take care with qualified terms, and have some theory of how to manage reference to terms in specific yearly versions. My recommendation for simple xref, would be (in this order) - A version of MeSH based on IAO taking into account the issues noted - A version of MeSH based on the Neurocommons version, which is SKOS-based, takes care with qualifiers, and is built direct from MeSH source, but not the versioning issues. - A direct link to the MeSH web space. - The current bioportal version (this falls under the line of recommended) -Alan > > Note there were some errors in the ID generation when we did this a while > back, so check the output URIs carefully if you go this route. > > No year though. Could probably add that. I think it would be great if we/OBO > could agree on a standard here though, there are numerous occasions to > reference MeSH for reasonable purposes. > > Cheers, > Melissa > > > On Dec 14, 2011, at 7:46 AM, David Osumi-Sutherland wrote: > > Hi all, > > We're in the process of mapping FlyBase publication type terms to MeSH. > This makes us consistent with PubMed - the main source of our biblio data. > > > Ideally I'd like to be able to make EquivalentClass links, but presumably > I'd need an up-to-date version of MeSH in OBO or OWL for that to be viable ? > If so, does anyone know if there is one available? > > In the absence of this, I've been looking at using the OBO xref mechanism > (which is also useful for attributing definitions.) > > Unfortunately, xrefs to MeSH are somewhat problematic. Here's the > GO.xrf_abbs entry: > > abbreviation: MeSH > database: Medical Subject Headings > object: MeSH heading > example_id: MeSH:mitosis > generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html > url_syntax: > http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id] > url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis > > Note the year embedded in the URL. It seems that the name/year combination > gives a stable reference. But to use this, we would need a new MeSH xref > abbreviation for each year. There's also a further wrinkle to this: > > "Cell Transformation, Neoplastic" > > > http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic > > This feels unsatisfactory, but I'm not sure there is any other good option. > > MeSH terms have unique IDs, but as far as I can gather, there is no way to > use these to roll a URL (although you can query them from here > http://www.nlm.nih.gov/mesh/2010/mesh_browser/MBrowser.html). > > Tree node IDs have been used by GO curators, e.g.: > > id: GO:0006927 > name: transformed cell apoptosis > namespace: biological_process > def: "The process of apoptosis in transformed cells, cells that have > undergone changes manifested by escape from control mechanisms, increased > growth potential, alterations in the cell surface, karyotypic abnormalities, > morphological and biochemical deviations from the norm." [GOC:jl, > MeSH:C04.697.152] > > These can be used to roll URLs in combination with a year and term name: > > http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic&field=entry#TreeC04.697.152 > > i.e.- they appear to only be useful for specifying which, of multiple > possible tree nodes for a term to display on linking. > > So - can we have year specific xrefs for MeSH in order to get reliable > expansions? It has the advantage of recording version information for free. > Or does anyone have a better suggestion? > > Cheers, > > David > > > > David Osumi-Sutherland, PhD > Ontologist > FlyBase / Virtual Fly Brain > Department of Genetics, > University of Cambridge, > Downing Street, > Cambridge, CB2 3EH, UK > Tel: +44 (0)1223 333 963 > Fax: +44 (0)1223 766 732 > http://www.virtualflybrain.org > > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format > > > Dr. Melissa Haendel > > eagle-i Networking Research Resources > OHSU Library http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology > Oregon Health & Science University > ha...@oh... > skype: melissa.haendel > 503-407-5970 > > > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/ > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format > |
From: David Osumi-S. <dj...@ge...> - 2011-12-14 13:29:06
|
Hi Melissa, You're up early! Thanks for the quick response. Looks very promising. ALL: Given that these NCBO purls resolve, would it be sensible to have an GO.xref_abbs entry that provides a shorthand for specifying the Bioportal URLs for MeSH terms? Any suggestions for what this should be? - David On 14 Dec 2011, at 13:17, Melissa Haendel wrote: > Hi David, > not sure if this is what you are looking for, but we've been able to get a MeSH taxonomy out of NCBO for use as a reference taxonomy in eagle-i using their view extractor tool: > http://www.bioontology.org/wiki/index.php/View_Extraction > > The classes look like this: > <!-- http://purl.bioontology.org/ontology/MSH/D000008 --> > > <owl:Class rdf:about="http://purl.bioontology.org/ontology/MSH/D000008"> > <rdfs:label>Abdominal Neoplasms</rdfs:label> > <rdfs:subClassOf rdf:resource="http://purl.bioontology.org/ontology/MSH/D009371"/> > </owl:Class> > > Note there were some errors in the ID generation when we did this a while back, so check the output URIs carefully if you go this route. > > No year though. Could probably add that. I think it would be great if we/OBO could agree on a standard here though, there are numerous occasions to reference MeSH for reasonable purposes. > > Cheers, > Melissa > > > On Dec 14, 2011, at 7:46 AM, David Osumi-Sutherland wrote: > >> Hi all, >> >> We're in the process of mapping FlyBase publication type terms to MeSH. This makes us consistent with PubMed - the main source of our biblio data. >> >> Ideally I'd like to be able to make EquivalentClass links, but presumably I'd need an up-to-date version of MeSH in OBO or OWL for that to be viable ? If so, does anyone know if there is one available? >> >> In the absence of this, I've been looking at using the OBO xref mechanism (which is also useful for attributing definitions.) >> >> Unfortunately, xrefs to MeSH are somewhat problematic. Here's the GO.xrf_abbs entry: >> >> abbreviation: MeSH >> database: Medical Subject Headings >> object: MeSH heading >> example_id: MeSH:mitosis >> generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html >> url_syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id] >> url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis >> >> Note the year embedded in the URL. It seems that the name/year combination gives a stable reference. But to use this, we would need a new MeSH xref abbreviation for each year. There's also a further wrinkle to this: >> >> "Cell Transformation, Neoplastic" >>> >> http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic >> >> This feels unsatisfactory, but I'm not sure there is any other good option. >> >> MeSH terms have unique IDs, but as far as I can gather, there is no way to use these to roll a URL (although you can query them from here http://www.nlm.nih.gov/mesh/2010/mesh_browser/MBrowser.html). >> >> Tree node IDs have been used by GO curators, e.g.: >> >> id: GO:0006927 >> name: transformed cell apoptosis >> namespace: biological_process >> def: "The process of apoptosis in transformed cells, cells that have undergone changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm." [GOC:jl, MeSH:C04.697.152] >> >> These can be used to roll URLs in combination with a year and term name: >> >> http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic&field=entry#TreeC04.697.152 >> >> i.e.- they appear to only be useful for specifying which, of multiple possible tree nodes for a term to display on linking. >> >> So - can we have year specific xrefs for MeSH in order to get reliable expansions? It has the advantage of recording version information for free. Or does anyone have a better suggestion? >> >> Cheers, >> >> David >> >> >> >> David Osumi-Sutherland, PhD >> Ontologist >> FlyBase / Virtual Fly Brain >> Department of Genetics, >> University of Cambridge, >> Downing Street, >> Cambridge, CB2 3EH, UK >> Tel: +44 (0)1223 333 963 >> Fax: +44 (0)1223 766 732 >> http://www.virtualflybrain.org >> >> >> ------------------------------------------------------------------------------ >> Cloud Computing - Latest Buzzword or a Glimpse of the Future? >> This paper surveys cloud computing today: What are the benefits? >> Why are businesses embracing it? What are its payoffs and pitfalls? >> http://www.accelacomm.com/jaw/sdnl/114/51425149/ >> _______________________________________________ >> Obo-format mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-format > > Dr. Melissa Haendel > > eagle-i Networking Research Resources > OHSU Library http://www.ohsu.edu/library/ > Department of Medical Informatics and Epidemiology > Oregon Health & Science University > ha...@oh... > skype: melissa.haendel > 503-407-5970 > > > ------------------------------------------------------------------------------ > Cloud Computing - Latest Buzzword or a Glimpse of the Future? > This paper surveys cloud computing today: What are the benefits? > Why are businesses embracing it? What are its payoffs and pitfalls? > http://www.accelacomm.com/jaw/sdnl/114/51425149/_______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss David Osumi-Sutherland, PhD Ontologist Virtual Fly Brain / FlyBase Department of Genetics University of Cambridge Downing Street Cambridge, CB2 3EH, UK +44 (0)1223 333 963 http://www.virtualflybrain.org |
From: Melissa H. <ha...@oh...> - 2011-12-14 13:17:43
|
Hi David, not sure if this is what you are looking for, but we've been able to get a MeSH taxonomy out of NCBO for use as a reference taxonomy in eagle-i using their view extractor tool: http://www.bioontology.org/wiki/index.php/View_Extraction The classes look like this: <!-- http://purl.bioontology.org/ontology/MSH/D000008 --> <owl:Class rdf:about="http://purl.bioontology.org/ontology/MSH/D000008"> <rdfs:label>Abdominal Neoplasms</rdfs:label> <rdfs:subClassOf rdf:resource="http://purl.bioontology.org/ontology/MSH/D009371"/> </owl:Class> Note there were some errors in the ID generation when we did this a while back, so check the output URIs carefully if you go this route. No year though. Could probably add that. I think it would be great if we/OBO could agree on a standard here though, there are numerous occasions to reference MeSH for reasonable purposes. Cheers, Melissa On Dec 14, 2011, at 7:46 AM, David Osumi-Sutherland wrote: Hi all, We're in the process of mapping FlyBase publication type terms to MeSH. This makes us consistent with PubMed - the main source of our biblio data. Ideally I'd like to be able to make EquivalentClass links, but presumably I'd need an up-to-date version of MeSH in OBO or OWL for that to be viable ? If so, does anyone know if there is one available? In the absence of this, I've been looking at using the OBO xref mechanism (which is also useful for attributing definitions.) Unfortunately, xrefs to MeSH are somewhat problematic. Here's the GO.xrf_abbs entry: abbreviation: MeSH database: Medical Subject Headings object: MeSH heading example_id: MeSH:mitosis generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html url_syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id] url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis Note the year embedded in the URL. It seems that the name/year combination gives a stable reference. But to use this, we would need a new MeSH xref abbreviation for each year. There's also a further wrinkle to this: "Cell Transformation, Neoplastic" http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic This feels unsatisfactory, but I'm not sure there is any other good option. MeSH terms have unique IDs, but as far as I can gather, there is no way to use these to roll a URL (although you can query them from here http://www.nlm.nih.gov/mesh/2010/mesh_browser/MBrowser.html). Tree node IDs have been used by GO curators, e.g.: id: GO:0006927 name: transformed cell apoptosis namespace: biological_process def: "The process of apoptosis in transformed cells, cells that have undergone changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm." [GOC:jl, MeSH:C04.697.152] These can be used to roll URLs in combination with a year and term name: http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic&field=entry#TreeC04.697.152 i.e.- they appear to only be useful for specifying which, of multiple possible tree nodes for a term to display on linking. So - can we have year specific xrefs for MeSH in order to get reliable expansions? It has the advantage of recording version information for free. Or does anyone have a better suggestion? Cheers, David David Osumi-Sutherland, PhD Ontologist FlyBase / Virtual Fly Brain Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK Tel: +44 (0)1223 333 963 Fax: +44 (0)1223 766 732 http://www.virtualflybrain.org ------------------------------------------------------------------------------ Cloud Computing - Latest Buzzword or a Glimpse of the Future? This paper surveys cloud computing today: What are the benefits? Why are businesses embracing it? What are its payoffs and pitfalls? http://www.accelacomm.com/jaw/sdnl/114/51425149/ _______________________________________________ Obo-format mailing list Obo...@li... https://lists.sourceforge.net/lists/listinfo/obo-format Dr. Melissa Haendel eagle-i Networking Research Resources OHSU Library http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology Oregon Health & Science University ha...@oh...<mailto:ha...@oh...> skype: melissa.haendel 503-407-5970 |
From: David Osumi-S. <dj...@ge...> - 2011-12-14 12:46:34
|
Hi all, We're in the process of mapping FlyBase publication type terms to MeSH. This makes us consistent with PubMed - the main source of our biblio data. Ideally I'd like to be able to make EquivalentClass links, but presumably I'd need an up-to-date version of MeSH in OBO or OWL for that to be viable ? If so, does anyone know if there is one available? In the absence of this, I've been looking at using the OBO xref mechanism (which is also useful for attributing definitions.) Unfortunately, xrefs to MeSH are somewhat problematic. Here's the GO.xrf_abbs entry: abbreviation: MeSH database: Medical Subject Headings object: MeSH heading example_id: MeSH:mitosis generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html url_syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id] url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis Note the year embedded in the URL. It seems that the name/year combination gives a stable reference. But to use this, we would need a new MeSH xref abbreviation for each year. There's also a further wrinkle to this: "Cell Transformation, Neoplastic" > http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic This feels unsatisfactory, but I'm not sure there is any other good option. MeSH terms have unique IDs, but as far as I can gather, there is no way to use these to roll a URL (although you can query them from here http://www.nlm.nih.gov/mesh/2010/mesh_browser/MBrowser.html). Tree node IDs have been used by GO curators, e.g.: id: GO:0006927 name: transformed cell apoptosis namespace: biological_process def: "The process of apoptosis in transformed cells, cells that have undergone changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm." [GOC:jl, MeSH:C04.697.152] These can be used to roll URLs in combination with a year and term name: http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Cell+Transformation,+Neoplastic&field=entry#TreeC04.697.152 i.e.- they appear to only be useful for specifying which, of multiple possible tree nodes for a term to display on linking. So - can we have year specific xrefs for MeSH in order to get reliable expansions? It has the advantage of recording version information for free. Or does anyone have a better suggestion? Cheers, David David Osumi-Sutherland, PhD Ontologist FlyBase / Virtual Fly Brain Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK Tel: +44 (0)1223 333 963 Fax: +44 (0)1223 766 732 http://www.virtualflybrain.org |
From: <obo...@go...> - 2011-12-13 23:38:08
|
Comment #2 on issue 60 by mcour...@gmail.com: Specification - section 2.1 http://code.google.com/p/oboformat/issues/detail?id=60 Looks better - I didn't see the expansion for NT though. Also maybe adding a reference to BNF? I went to check the wikipedia page http://en.wikipedia.org/wiki/Backus%E2%80%93Naur_Form which states "Terminals may appear in bold and NonTerminals in plain text rather than using italics and angle brackets." Though non normative, they say this is a commonly used rule. Do you abide by another standard/reference? |
From: <obo...@go...> - 2011-12-13 01:35:43
|
Comment #1 on issue 60 by cmung...@gmail.com: Specification - section 2.1 http://code.google.com/p/oboformat/issues/detail?id=60 Improved the docs, described what the acronyms stand for, and fixed some bold font issues. All non-terminals (NTs) should be in bold. See what you think: http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#BNF |