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From: Larisa S. [lss] <ls...@ab...> - 2012-02-27 18:13:14
|
' 27 Feb''' Chair: Larissa Attended: BP, LS, Jie, James Overton, Philippe, Chris Stoeckert, Melissa,Trish Whetzel, Marcus, Carlo, Zvita, Matthew Brush, Jen Fostel, 1. Jie: A reprt from the subgroup meeting about phenotype assessment AI: Jie - prepare and post a short report on the subgroup work. Shortly report of RCN: Plant people are interested in modeling metadata using OBI framework. I am in contact for this. They are also thinking to collect experimental condition. OBI can help in providing terms in annotations. Currently, they really want us to help in "growth condition" (modeling and annotation). Suggestion: subgroups should post short reports about their work and the results for the OBI dev. Subgroups activities should be better recognized and acknowledged. On the related issue: people are having difficulty using OBI, e.g. developing annotation forms, contributing terms, alignning their existing ontology with OBI, etc. We need to think about better tutorial, regular help line, assistance, etc. 2. the Revision of the OBI organizational structure. The documents has been accepted by the majority (only 1 vote against). The document will beposted on-line. There were worth considering comments on the document made. AI: LS - incorporate suggestions to improve the document and send an updated version to BP in a week. AI: ALL -assign yourself to the tasks: http://obi-ontology.org/page/Task add new tasks if needed |
From: Larisa S. [lss] <ls...@ab...> - 2012-02-27 09:59:16
|
yes, we should discuss that. Summary of the comments and points to discuss: 1. should be subgroup activities added to the active developers roles? 2. shall we confirm 2 weeks period (it was the opinion on the previous call). 3. how/who will control the status of an active/ not active developer? 4. OBI papers authorship. It is not clear why the 1st paper will include all the developers and others only active developers. 5. papers with contribution from OBI. The OBI Consortium has an authorship right with all consequences. 6. obi.owl contributors. Should we ask permission to include people as contributors? again who and how control the active developer status? 7. Not many added initials to the tasks. ________________________________________ From: Chris Stoeckert [sto...@pc...] Sent: Sunday, February 26, 2012 8:54 PM To: Larisa Soldatova [lss] Cc: OBI Developers; OBI Coordinators Subject: Re: [Obi-devel] agenda for the 27.2 call? Another item is the vote on the Revision of the OBI organizational structure. According to the Votes page, the vote closes on the 27th. http://obi-ontology.org/page/Votes As part of that item we can address comments made to the associated document. https://docs.google.com/a/apidb.org/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit?disco=AAAAAEQJ1wY Cheers, Chris On Feb 26, 2012, at 1:43 PM, Larisa Soldatova [lss] wrote: > Hi All, > > Do you have suggestions for the agenda? > > There is one point so far: > > 1. Report from the subgroup meeting about phenotype assessment. > > We can go through the items tracker. > > Speak to you soon, > Larisa > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel |
From: Chris S. <sto...@pc...> - 2012-02-26 20:54:46
|
Another item is the vote on the Revision of the OBI organizational structure. According to the Votes page, the vote closes on the 27th. http://obi-ontology.org/page/Votes As part of that item we can address comments made to the associated document. https://docs.google.com/a/apidb.org/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit?disco=AAAAAEQJ1wY Cheers, Chris On Feb 26, 2012, at 1:43 PM, Larisa Soldatova [lss] wrote: > Hi All, > > Do you have suggestions for the agenda? > > There is one point so far: > > 1. Report from the subgroup meeting about phenotype assessment. > > We can go through the items tracker. > > Speak to you soon, > Larisa > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel |
From: Jie Z. <jie...@pc...> - 2012-02-13 18:00:30
|
Use this link: http://obi-ontology.org/w/index.php?title=Votes - Jie On 2/13/2012 12:21 PM, Bjoern Peters wrote: > Please put in your initials on > http://obi-ontology.org/w/index.php?title=Votes&oldid=5216 > To vote on the document describing the new OBI organizational structure. > The vote is open until Feb 27. > > - Bjoern > > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > > > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel |
From: Bjoern P. <bp...@li...> - 2012-02-13 17:23:47
|
Please put in your initials on http://obi-ontology.org/w/index.php?title=Votes&oldid=5216 To vote on the document describing the new OBI organizational structure. The vote is open until Feb 27. - Bjoern |
From: Jessica T. <jt...@mr...> - 2012-02-08 16:34:39
|
That looks like a very reasonable evolution of the system to me. (Though I guess I should put that in the comments on the link below...) Thanks, Jess On Tue, Feb 7, 2012 at 1:30 PM, Bjoern Peters <bp...@li...> wrote: > I have completed my final draft of the new OBI organizational structure > writeup. Please use the link below to comment on it before 2/13. After that > edits will be incorporated, and the document will be put up for a community > vote starting 2/20 and ending 3/5. Please do not wait for the voting to > start before you reading the draft. Here is an excerpt: > > *Preface: Historically decisions in OBI were made by ‘community > representatives’ who spoke for groups of researchers. This has been useful > to get OBI started, as it gave all communities an equal voice and it made > OBI into a truly cross-community effort. More recently with the OBI project > maturing, it has become clear that this structure can be a hindrance to > involve and reward those people that actively contribute to OBI but may not > be the sole representative of a clearly defined scientific community. > Therefore, we have decided to officially overhaul the OBI organizational > structure and make it ‘developer centric’, so that all individuals that > actively contribute to OBI participate equally in decision making. > > After this document has been accepted, we will retire the OBI > ‘coordinator’ status, mailing lists, and the ‘community representatives’ > concept.* > > > https://docs.google.com/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit?hl=en_US > > > - Bjoern > > -- > Bjoern Peters > Assistant Professor > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle > La Jolla, CA 92037, USA > Tel: 858/752-6914 > Fax: 858/752-6987 > http://www.liai.org/pages/faculty-peters > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel > > -- Jessica Turner, Ph.D. Associate Professor, Translational Neuroscience Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106 New Ph: 505-272-2869 email: jt...@mr... |
From: Bjoern P. <bp...@li...> - 2012-02-07 20:30:47
|
I have completed my final draft of the new OBI organizational structure writeup. Please use the link below to comment on it before 2/13. After that edits will be incorporated, and the document will be put up for a community vote starting 2/20 and ending 3/5. Please do not wait for the voting to start before you reading the draft. Here is an excerpt: Preface: Historically decisions in OBI were made by ‘community representatives’ who spoke for groups of researchers. This has been useful to get OBI started, as it gave all communities an equal voice and it made OBI into a truly cross-community effort. More recently with the OBI project maturing, it has become clear that this structure can be a hindrance to involve and reward those people that actively contribute to OBI but may not be the sole representative of a clearly defined scientific community. Therefore, we have decided to officially overhaul the OBI organizational structure and make it ‘developer centric’, so that all individuals that actively contribute to OBI participate equally in decision making. After this document has been accepted, we will retire the OBI ‘coordinator’ status, mailing lists, and the ‘community representatives’ concept. https://docs.google.com/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit?hl=en_US - Bjoern -- Bjoern Peters Assistant Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
From: Bjoern P. (G. Docs) <bp...@li...> - 2012-01-08 21:32:18
|
I've shared an item with you: OBI organizational structure https://docs.google.com/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit?invite=CMaQxsIC It's not an attachment -- it's stored online at Google Docs. To open this document, just click the link above. |
From: jie z. <jie...@pc...> - 2012-01-08 21:07:14
|
Sure. Thanks! Jie On 1/8/2012 4:04 PM, Bjoern Peters wrote: > https://docs.google.com/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit > |
From: Bjoern P. <bp...@li...> - 2012-01-08 21:04:57
|
As per my action item, I started putting my thoughts together here: https://docs.google.com/document/d/1NWms5Zxo0BDWezIHO86Z4yh9qqjLCYdCgjwBzd2s-Xs/edit Jie, can we add this to the agenda tomorrow? Thanks, Bjoern -- Bjoern Peters Assistant Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
From: jie z. <jie...@pc...> - 2011-12-16 14:28:43
|
Dear Suzanna, I have got approval from OBI group and would like to confirm that I will attend the RCN meeting as a representative of OBI. Thanks for the invitation. Best regard, Jie On 12/4/2011 8:27 PM, jie zheng wrote: > Dear Suzanna, > > Thanks a lot for your invitation. I am really willing to attend the > RCN meeting as a representative of OBI. I will discuss with OBI > coordinators and developers to see whether it works for them. Then I > will let you know our final decision as soon as possible. > > Best regards, > > Jie > > On 12/4/2011 8:03 PM, Suzanna Lewis wrote: >> Dear Jie, >> >> I would like to invite you, or at least one representative from OBI, >> to participate in the second annual summit meeting of the Phenotype >> Ontology RCN. The meeting will be held at the National Evolutionary >> Synthesis Center in Durham, NC, February 23-25, 2012. >> >> The Phenotype Ontology RCN (http://phenotypercn.org) was funded by >> NSF to establish a network of scientists who are developing (or would >> like to develop) phenotype ontologies. In contrast to the many >> well-established ontologies in the molecular community, the >> representation of morphology, behavior and other phenotypic traits >> using ontologies is in its infancy. Such ontologies, however, have >> the potential to integrate phenotype with data across all levels of >> the biological hierarchy. This RCN is building a community that, >> because of its domain expertise, sets the standards and best >> practices for the development of phenotype ontologies and a vision >> for their utility. >> >> The main focus of this meeting will be introduce and establish >> communication between scientists from several different research >> backgrounds including comparative evolutionary biologists, model >> organism biologists, applied scientists, and ontology developers and >> logicians. We will be introducing concepts involved in developing >> and coordinating ontologies as well as ontology annotation. >> >> At this point, we¹d like to know whether you would be able to >> participate in this meeting? We plan to begin on Thursday morning, >> February 23 (you >> would arrive Wednesday evening) and work through Saturday noon, >> February 25th. All travel, lodging and food expenses will be covered >> by the RCN. I saw on the mailing list that the OBI group has some >> interest in phenotype annotation we are quite eager to have you join >> us! (We are, after all, funded to assist in coordination). >> >> Sincerely, Suzanna > |
From: Bjoern P. <bp...@li...> - 2011-12-06 15:52:25
|
Thanks for the all the (mostly off-list) emails! To answer one question that came up repeatedly: Yes, I do plan to continue to contribute to OBI long term, but at a significantly reduced workload. Best, Bjoern ----- Original Message ----- > Ah, no! > Bjoern was our great leader for so many years. It just never would be > the same. Everyone understands the imperative of other commitments, > of course. But maybe Bjoern can just have a break or less OBI load > for the period of other grants? > Larisa > ________________________________________ > From: Bjoern Peters [bp...@li...] > Sent: Monday, December 05, 2011 4:19 PM > To: obi-coord ; OBI Developers > Subject: [Obi-devel] retiring > All, > Over the past months, I noticed that I am not doing a good enough job > any more for OBI. I have not managed to resolve my action items in a > timely manner, and have not managed to move forward with the > manuscript writing. This is mainly because I have too many other > ongoing projects, and OBI needs to fit into my 'spare time'. This > will get worse, as work on another recently funded grant kicks in > for me. Worst of all, I have started to get unreasonably annoyed > when things aren't 'moving my way'. I think OBI will be better of if > someone takes over the official OBO foundry representative position > who is working on ontologies full time. > I want to minimize disruption and want to bring things that I started > to completion, so I am not planning to drop everything I did > immediately. I would like to begin the process of transition though, > and we need to clarify the process for that. > - Bjoern > -- > Bjoern Peters > Assistant Professor > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle > La Jolla, CA 92037, USA > Tel: 858/752-6914 > Fax: 858/752-6987 > http://www.liai.org/pages/faculty-peters |
From: Larisa S. [lss] <ls...@ab...> - 2011-12-06 07:23:12
|
Ah, no! Bjoern was our great leader for so many years. It just never would be the same. Everyone understands the imperative of other commitments, of course. But maybe Bjoern can just have a break or less OBI load for the period of other grants? Larisa ________________________________________ From: Bjoern Peters [bp...@li...] Sent: Monday, December 05, 2011 4:19 PM To: obi-coord ; OBI Developers Subject: [Obi-devel] retiring All, Over the past months, I noticed that I am not doing a good enough job any more for OBI. I have not managed to resolve my action items in a timely manner, and have not managed to move forward with the manuscript writing. This is mainly because I have too many other ongoing projects, and OBI needs to fit into my 'spare time'. This will get worse, as work on another recently funded grant kicks in for me. Worst of all, I have started to get unreasonably annoyed when things aren't 'moving my way'. I think OBI will be better of if someone takes over the official OBO foundry representative position who is working on ontologies full time. I want to minimize disruption and want to bring things that I started to completion, so I am not planning to drop everything I did immediately. I would like to begin the process of transition though, and we need to clarify the process for that. - Bjoern -- Bjoern Peters Assistant Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
From: Bjoern P. <bp...@li...> - 2011-12-05 16:19:42
|
All, Over the past months, I noticed that I am not doing a good enough job any more for OBI. I have not managed to resolve my action items in a timely manner, and have not managed to move forward with the manuscript writing. This is mainly because I have too many other ongoing projects, and OBI needs to fit into my 'spare time'. This will get worse, as work on another recently funded grant kicks in for me. Worst of all, I have started to get unreasonably annoyed when things aren't 'moving my way'. I think OBI will be better of if someone takes over the official OBO foundry representative position who is working on ontologies full time. I want to minimize disruption and want to bring things that I started to completion, so I am not planning to drop everything I did immediately. I would like to begin the process of transition though, and we need to clarify the process for that. - Bjoern -- Bjoern Peters Assistant Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
From: jie z. <jie...@pc...> - 2011-12-05 01:27:09
|
Dear Suzanna, Thanks a lot for your invitation. I am really willing to attend the RCN meeting as a representative of OBI. I will discuss with OBI coordinators and developers to see whether it works for them. Then I will let you know our final decision as soon as possible. Best regards, Jie On 12/4/2011 8:03 PM, Suzanna Lewis wrote: > Dear Jie, > > I would like to invite you, or at least one representative from OBI, to participate in the second annual summit meeting of the Phenotype Ontology RCN. The meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, February 23-25, 2012. > > The Phenotype Ontology RCN (http://phenotypercn.org) was funded by NSF to establish a network of scientists who are developing (or would like to develop) phenotype ontologies. In contrast to the many well-established ontologies in the molecular community, the representation of morphology, behavior and other phenotypic traits using ontologies is in its infancy. Such ontologies, however, have the potential to integrate phenotype with data across all levels of the biological hierarchy. This RCN is building a community that, because of its domain expertise, sets the standards and best practices for the development of phenotype ontologies and a vision for their utility. > > The main focus of this meeting will be introduce and establish communication between scientists from several different research backgrounds including comparative evolutionary biologists, model organism biologists, applied scientists, and ontology developers and logicians. We will be introducing concepts involved in developing and coordinating ontologies as well as ontology annotation. > > At this point, we¹d like to know whether you would be able to participate in this meeting? We plan to begin on Thursday morning, February 23 (you > would arrive Wednesday evening) and work through Saturday noon, February 25th. All travel, lodging and food expenses will be covered by the RCN. I saw on the mailing list that the OBI group has some interest in phenotype annotation we are quite eager to have you join us! (We are, after all, funded to assist in coordination). > > Sincerely, Suzanna |
From: Suzanna L. <su...@be...> - 2011-12-05 01:03:39
|
Dear Jie, I would like to invite you, or at least one representative from OBI, to participate in the second annual summit meeting of the Phenotype Ontology RCN. The meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, February 23-25, 2012. The Phenotype Ontology RCN (http://phenotypercn.org) was funded by NSF to establish a network of scientists who are developing (or would like to develop) phenotype ontologies. In contrast to the many well-established ontologies in the molecular community, the representation of morphology, behavior and other phenotypic traits using ontologies is in its infancy. Such ontologies, however, have the potential to integrate phenotype with data across all levels of the biological hierarchy. This RCN is building a community that, because of its domain expertise, sets the standards and best practices for the development of phenotype ontologies and a vision for their utility. The main focus of this meeting will be introduce and establish communication between scientists from several different research backgrounds including comparative evolutionary biologists, model organism biologists, applied scientists, and ontology developers and logicians. We will be introducing concepts involved in developing and coordinating ontologies as well as ontology annotation. At this point, we¹d like to know whether you would be able to participate in this meeting? We plan to begin on Thursday morning, February 23 (you would arrive Wednesday evening) and work through Saturday noon, February 25th. All travel, lodging and food expenses will be covered by the RCN. I saw on the mailing list that the OBI group has some interest in phenotype annotation we are quite eager to have you join us! (We are, after all, funded to assist in coordination). Sincerely, Suzanna |
From: <phi...@ne...> - 2011-09-13 12:05:38
|
Chris Almost none of this has been tested in court, so it's almost impossible to say. Combined with the reality that the authors are multinational, the answer is likely to be slightly different in every different environment. Most of the authors are employed by organizations; so those sections written by US authors are probably copyright by their organisations whether they claim them or not, as they works for hire. There is a roughly similar thing in the UK. Except for those people who work at EBI which is physically in the UK, but legally in some strange EU never-land. As I see it, the Creative Commons license is an aspiration and a hope; that is, it is unlikely any of our employers will assert copyright control in a negative way. Given that any such assertion of rights would probably remove any value that that OBI has, this is not an unreasonable hope, as it isn't really in anyones interest to do so. Which doesn't mean that they wouldn't. Patents -- well, who knows there. Patent law is even more jurisdictional than copyright. Phil Christopher Pepe <chr...@gm...> writes: > My name is Chris Pepe and I am a third year law student at American > University in Washington, DC. I am currently researching the intellectual > property aspect of technology standardizations and had a few questions about > your organization. It appears that your project is a collaboration of many > organizations. Do any of the organizations claim copyright or patent rights > over the work product that your project produces, or does the Creative > Commons license govern any patent or copyright rights that might arise from > your work? Do the organizations that provide funding for your project place > any copyright or patent restrictions/requirements on the work product that > your project produces? I would greatly appreciate any information that you > could provide me. |
From: James M. <ma...@eb...> - 2011-09-12 08:22:21
|
Chris, OBI, the ontology, is open and free to use. So I think the simple answer is no, there are no copyright or patent rights held over the ontology, other than those specified in the CC license. Best, James On 11/09/2011 14:48, Christopher Pepe wrote: > > Hello, > > My name is Chris Pepe and I am a third year law student at American > University in Washington, DC. I am currently researching the > intellectual property aspect of technology standardizations and had a > few questions about your organization. It appears that your project > is a collaboration of many organizations. Do any of the organizations > claim copyright or patent rights over the work product that your > project produces, or does the Creative Commons license govern any > patent or copyright rights that might arise from your work? Do the > organizations that provide funding for your project place any > copyright or patent restrictions/requirements on the work product that > your project produces? I would greatly appreciate any information that > you could provide me. > > > Sincerely, > > Chris Pepe > > > ------------------------------------------------------------------------------ > Doing More with Less: The Next Generation Virtual Desktop > What are the key obstacles that have prevented many mid-market businesses > from deploying virtual desktops? How do next-generation virtual desktops > provide companies an easier-to-deploy, easier-to-manage and more affordable > virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > > > _______________________________________________ > Obi-coord mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-coord -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
From: Christopher P. <chr...@gm...> - 2011-09-11 13:49:03
|
Hello, My name is Chris Pepe and I am a third year law student at American University in Washington, DC. I am currently researching the intellectual property aspect of technology standardizations and had a few questions about your organization. It appears that your project is a collaboration of many organizations. Do any of the organizations claim copyright or patent rights over the work product that your project produces, or does the Creative Commons license govern any patent or copyright rights that might arise from your work? Do the organizations that provide funding for your project place any copyright or patent restrictions/requirements on the work product that your project produces? I would greatly appreciate any information that you could provide me. Sincerely, Chris Pepe |
From: Chris S. <sto...@pc...> - 2011-08-26 17:28:21
|
I've started a page to provide information about the upcoming workshop Oct 12-14 at Penn in Philadelphia. See http://obi-ontology.org/page/Philly2011 If you plan on coming and want to stay in walking distance, please go ahead and book your hotel. For some reason rooms were hard to find when we did this around the same time in 2009 so make sure you can get one this time around! Cheers, Chris |
From: Chris S. <sto...@pc...> - 2011-08-15 16:38:53
|
1. OBI workshop in Philadelphia. Date will be decided by next week's call: Monday August 22. Please put your preferences in Doodle if you want them considered. http://doodle.com/6wxd3kesmge94v94 2. OBI grant proposal. General discussion of submissions and plans forward. Everyone will benefit but need to put together a story that shows overlap between needs of projects and include projects for which OBI is essential. All are expected to help review and edit the grant however need to have a few people who will drive the writing. No way to make the Sept. deadline so now looking at Jan. Volunteers for driving the writing are Bjoern, Marcus, Larisa, Carlo/ Melissa, Jess, Susanna/Philippe, and me (Chris). I'll set up a doodle poll for the week of the 29th - if you really want to commit many hours of work on this but were not on the call, please let me know. 3. No news on the OBI paper. Cheers, Chris |
From: Susanna-Assunta S. <sa....@gm...> - 2011-08-15 15:21:28
|
1. Projects you would interface with: *Biosharing* (biosharing.org) and *ISAcommunities* (isa-tools.org) 1.1 What would be OBI deliverables? The Biosharing catalogue needs descriptors for assay, data types and study descriptors with the aim of facilitating search and consistent descriptions across resources. ISA user communities ranges over different life science domains and technologies, gaps and overlaps in terminologies need to be overcome. 1.1 How do these overlap or complement existing funding for those needs: Some overlap with existing with effort such as NIFSTD, BRO and EDAM. OBI currently provides a set of descriptors but gaps in coverage need closing. 2. Terminologies to add: Addition to support NGS, Metabolomics, Phylogenetics and Biodiversity studies, environmental genomics. Addition to support stem cell research Addition to support plant research What would this enable? Facilitate consistency description across different life science domains (i) minimum information checklists and (ii) datasets. 3. tools to work on NCBO Annotator Extension to QTT support to facilitate batch import, Work with Protege Team and ontology component of ISA framework. Maintain a library a QTT patterns under the OBI framework Funding: BioSharing and ISA are funded for 2.5 more years by BBSRC and NERC; we have just got another 3 years on related project that would support also these activities. However, there are not targeted funds for ontology building (addressing gaps and overalps) and certainly would not support OBI directly. Susanna On 15/08/2011 13:21, Susanna-Assunta Sansone wrote: > Hi Chris, > we are also interested in exploring participating in this proposal; > more on the call later. > Both BioSharing (biosharing.org; extending on the MIBBI effort) and > ISA communities (isa-tools.org; ranging from stem cell discovery, > metabolomics and metagenomics) would be relevant case studies. > University of Oxford has a DUNS number, even if I do not have (yet) a > eRA Commons User Account. > Susanna > > On 14/08/2011 18:59, Chris Stoeckert wrote: >> We'll focus on going over the submissions for the grant (due today) and how to decide what will make the strongest proposal. >> Any other items? >> >> Thanks >> Chris >> ------------------------------------------------------------------------------ >> FREE DOWNLOAD - uberSVN with Social Coding for Subversion. >> Subversion made easy with a complete admin console. Easy >> to use, easy to manage, easy to install, easy to extend. >> Get a Free download of the new open ALM Subversion platform now. >> http://p.sf.net/sfu/wandisco-dev2dev >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel > > -- > Susanna-Assunta Sansone, PhD > > Team Leader > University of Oxford > > Projects:www.isa-tools.org|www.mibbi.org|www.biosharing.org > > University of Oxford Tel: +44(0)1865 610622 > Oxford e-Research Centre Fax: +44(0)1865 610612 > 7 Keble Road, Oxford skype: susanna-a.sansone > OX1 3QG, UK uk.linkedin.com/in/sasansone > -- > > > ------------------------------------------------------------------------------ > uberSVN's rich system and user administration capabilities and model > configuration take the hassle out of deploying and managing Subversion and > the tools developers use with it. Learn more about uberSVN and get a free > download at: http://p.sf.net/sfu/wandisco-dev2dev > > > _______________________________________________ > Obi-coord mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-coord |
From: Chris S. <sto...@pc...> - 2011-08-15 13:13:47
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Thanks Susanna. Can you provide a description according to needs, deliverables, funding, terminologies, tools as others have done? Otherwise it is difficult to compare and integrate. Chris On Aug 15, 2011, at 8:21 AM, Susanna-Assunta Sansone wrote: > Hi Chris, > we are also interested in exploring participating in this proposal; more on the call later. > Both BioSharing (biosharing.org; extending on the MIBBI effort) and ISA communities (isa-tools.org; ranging from stem cell discovery, metabolomics and metagenomics) would be relevant case studies. > University of Oxford has a DUNS number, even if I do not have (yet) a eRA Commons User Account. > Susanna > > On 14/08/2011 18:59, Chris Stoeckert wrote: >> >> We'll focus on going over the submissions for the grant (due today) and how to decide what will make the strongest proposal. >> Any other items? >> >> Thanks >> Chris >> ------------------------------------------------------------------------------ >> FREE DOWNLOAD - uberSVN with Social Coding for Subversion. >> Subversion made easy with a complete admin console. Easy >> to use, easy to manage, easy to install, easy to extend. >> Get a Free download of the new open ALM Subversion platform now. >> http://p.sf.net/sfu/wandisco-dev2dev >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel > > -- > Susanna-Assunta Sansone, PhD > > Team Leader > University of Oxford > > Projects: www.isa-tools.org|www.mibbi.org|www.biosharing.org > > University of Oxford Tel: +44(0)1865 610622 > Oxford e-Research Centre Fax: +44(0)1865 610612 > 7 Keble Road, Oxford skype: susanna-a.sansone > OX1 3QG, UK uk.linkedin.com/in/sasansone > -- |
From: Susanna-Assunta S. <sa....@gm...> - 2011-08-15 12:21:29
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Hi Chris, we are also interested in exploring participating in this proposal; more on the call later. Both BioSharing (biosharing.org; extending on the MIBBI effort) and ISA communities (isa-tools.org; ranging from stem cell discovery, metabolomics and metagenomics) would be relevant case studies. University of Oxford has a DUNS number, even if I do not have (yet) a eRA Commons User Account. Susanna On 14/08/2011 18:59, Chris Stoeckert wrote: > We'll focus on going over the submissions for the grant (due today) and how to decide what will make the strongest proposal. > Any other items? > > Thanks > Chris > ------------------------------------------------------------------------------ > FREE DOWNLOAD - uberSVN with Social Coding for Subversion. > Subversion made easy with a complete admin console. Easy > to use, easy to manage, easy to install, easy to extend. > Get a Free download of the new open ALM Subversion platform now. > http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel -- Susanna-Assunta Sansone, PhD Team Leader University of Oxford Projects: www.isa-tools.org|www.mibbi.org|www.biosharing.org University of Oxford Tel: +44(0)1865 610622 Oxford e-Research Centre Fax: +44(0)1865 610612 7 Keble Road, Oxford skype: susanna-a.sansone OX1 3QG, UK uk.linkedin.com/in/sasansone -- |
From: James M. <ma...@eb...> - 2011-08-15 11:50:47
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Hi Chris, I'm not sure what we can offer this end, but any letters of support etc. will be readily forthcoming. We use OBI here so are active consumers and we have started using it in our RDF representations of Gene Expression Atlas too. Please let me know if you need more from me; I presume the project descriptions people were sending were going to be actively involved as part of the grant. We're happy to be involved in some way. Regarding the views that have been mentioned, we have a grant with NCBO starting this month which has a component to produce views for curation (actually more than just views, but views is a subset of our objectives). The implementation will start in November. OBI will form a component of the views along with several others. I know I mentioned this at the grant meeting in Buffalo but I wanted to mention this again as we have resources to do this work so we can support most of OBI's needs I'd imagine. If this is of interest to the group we'd be happy to include something on this in some form. Cheers, James On 14/08/2011 18:59, Chris Stoeckert wrote: > We'll focus on going over the submissions for the grant (due today) and how to decide what will make the strongest proposal. > Any other items? > > Thanks > Chris > ------------------------------------------------------------------------------ > FREE DOWNLOAD - uberSVN with Social Coding for Subversion. > Subversion made easy with a complete admin console. Easy > to use, easy to manage, easy to install, easy to extend. > Get a Free download of the new open ALM Subversion platform now. > http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |