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From: Trish W. <wh...@st...> - 2011-05-11 16:26:27
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Trish W. <wh...@st...> - 2011-05-11 16:11:48
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Trish W. <wh...@st...> - 2011-04-28 18:24:55
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Trish W. <wh...@st...> - 2011-04-22 00:45:35
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The Support mailing list is now open for subscription [1] and is also archived [2] for review of past questions and comments. Trish [1] https://mailman.stanford.edu/mailman/listinfo/bioontology-support [2] http://www.bioontology.org/bioontology-support-archive _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Tomasz A. <to...@eb...> - 2011-04-06 16:13:44
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Dear EFO Users, EFO version 2.12.1 has now been released. For download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl http://www.ebi.ac.uk/efo/efo.obo Release notes are available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view is available from: http://www.ebi.ac.uk/efo/efo_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- Tomasz Adamusiak, MD, PhD European Bioinformatics Institute +44 (0) 1223 492 562 tom...@eb... |
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From: James M. <ma...@eb...> - 2011-03-21 17:16:04
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Dear EFO Users, EFO version 2.12 has now been released. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl Release notes are available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view is available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
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From: James M. <ma...@eb...> - 2011-02-28 11:49:44
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Dear users, A new version of the EFO SourceForge pages is now available. http://efo.sourceforge.net/ James -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
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From: Trish W. <wh...@st...> - 2011-02-20 06:48:13
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Since BioPortal (http://bioportal.bioontology.org/) is now able to load an ontology file given a URL vs. the previous method of connecting into a CVS/SVN repository, we are changing how we extract the ontology version information. For OBO format ontologies, we will extract this information from the property "data-version" based on the property description here: http://www.geneontology.org/GO.format.obo-1_4.shtml. For OWL ontologies, we will extract the version information from owl:versioninfo. In your next ontology release, can you include the version information in the ontology file? Also, is someone from your group subscribed to receive comments on your ontology via the email alert feature? To subscribe, please send email to su...@bi... with the ontology name and email address to subscribe. Thanks! Trish Trish Whetzel, PhD Outreach Coordinator The National Center for Biomedical Ontology Ph: 650-721-2378 wh...@st... http://www.bioontology.org |
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From: James M. <ma...@eb...> - 2011-02-15 16:56:09
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Dear EFO Users, EFO version 2.11 has now been released. Please not releases are now scheduled for the 15th of every month. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl Release notes are available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view is available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
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From: Tomasz A. <tom...@eb...> - 2011-01-21 17:14:02
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Dear EFO Users, EFO version 2.10 has now been released. For the OWL and OBO versions of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl http://www.ebi.ac.uk/efo/efo.obo Release notes: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view of the ontology: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- Tomasz Adamusiak, MD, PhD European Bioinformatics Institute +44 (0) 1223 492 562 tom...@eb... |
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From: Tomasz A. <tom...@eb...> - 2011-01-21 17:08:04
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Dear EFO Users, EFO version 2.10 has now been released. For the OWL and OBO versions of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl http://www.ebi.ac.uk/efo/efo.obo Release notes: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view of the ontology: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- Tomasz Adamusiak, MD, PhD European Bioinformatics Institute +44 (0) 1223 492 562 tom...@eb... |
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From: Tomasz A. <to...@eb...> - 2010-12-02 21:18:19
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Dear EFO Users, EFO version 2.9 has now been released. For the OWL and OBO versions of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl http://www.ebi.ac.uk/efo/efo.obo Release notes: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view of the ontology: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: Tomasz A. <to...@eb...> - 2010-11-15 16:40:43
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Apologies. Accidentally sent it to the wrong mailing list. Cheers Tomasz On 15/11/2010 16:38, Tomasz Adamusiak wrote: > Dear OntoCAT Users, > > OntoCAT version 0.9.6 has now been released. You can download it from > (under release): > > https://sourceforge.net/projects/ontocat/files/ > > In this release: > - Updated OWL API dependence to 3.1 > -On creation of FileOntologyService you can specify a user-defined > ontology accession > - New utils package containing convenience methods for the R ontocat package > - BioportalOntologyService .getOntologies() now includes the ontology views > - FIX: Unnecessary warnings when searching OLS > - FIX: Occasional incorrect parsing of ontology accessions when > searching OLS > - FIX: FileOntologyService throwing an exception if there were classes > with no properties > > Many thanks, > > OntoCAT Dev Team > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > EFO-users mailing list > EFO...@li... > https://lists.sourceforge.net/lists/listinfo/efo-users |
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From: Tomasz A. <to...@eb...> - 2010-11-15 16:38:24
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Dear OntoCAT Users, OntoCAT version 0.9.6 has now been released. You can download it from (under release): https://sourceforge.net/projects/ontocat/files/ In this release: - Updated OWL API dependence to 3.1 -On creation of FileOntologyService you can specify a user-defined ontology accession - New utils package containing convenience methods for the R ontocat package - BioportalOntologyService .getOntologies() now includes the ontology views - FIX: Unnecessary warnings when searching OLS - FIX: Occasional incorrect parsing of ontology accessions when searching OLS - FIX: FileOntologyService throwing an exception if there were classes with no properties Many thanks, OntoCAT Dev Team |
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From: James M. <ma...@eb...> - 2010-11-04 13:54:06
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Dear EFO Users, EFO version 2.8 has now been released. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl Release notes are available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view is available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
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From: Tomasz A. <to...@eb...> - 2010-10-11 18:00:43
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Dear EFO Users, EFO version 2.7 has now been released. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl Release notes are available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/docs/releasedocs/ExFactor%20Ontology%20release%20notes.txt Inferred view is available from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: Tomasz A. <to...@eb...> - 2010-09-01 17:23:13
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Dear EFO Users, EFO version 2.6 has now been released. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-06-30 13:17:53
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Dear Users, EFO release 2.4 is now available at http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/ Updates to tooling will form a major component of the next EFO release. EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 494 468 |
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From: Tomasz A. <to...@eb...> - 2010-04-13 15:01:28
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Dear EFO Users, EFO version 2.2 has now been released. For OWL download of the ontology please see: http://www.ebi.ac.uk/efo/efo.owl For web based viewing and other details see EFO homepage http://www.ebi.ac.uk/efo http://www.ebi.ac.uk/efo/overview Many Thanks EFO Dev Team -- European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge, CB10 1SD United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-03-10 13:48:14
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A 2.1.1 interim release of EFO has now gone live to correct for a known bug in some external import closures. This does not affect provenance or introduce any new obsolescence to the ontology. Many thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-03-04 09:31:07
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Dear All, Release 2.1 of EFO is now live. Please see www.ebi.ac.uk/efo for details. This release completes some major changes to importing external classes from ChEBI, NCBI Taxon and Unit Ontology. Many thanks, EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-02-11 17:34:53
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Dear Users, Continuing the import changes to EFO, some further imports from NCBI Taxon are now included in the 2.0.1 release. See release notes for details. EFO Dev Team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-02-08 16:52:01
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EFO version 2.0 is released today with some major changes to class imports. Please see release docs for full details. Available from http://efo.svn.sourceforge.net/viewvc/efo/trunk/ Best, EFO Release team -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-01-25 18:04:39
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A new version of the software ontology has been released to SourceForge site http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/softwareontologyinowl/ This contains OBI and IAO classes and properties for integration to OBO Foundry ontologies. This will be visible in BioPortal tomorrow morning. Regards, James -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: James M. <ma...@eb...> - 2010-01-25 16:08:44
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label: information definition: Information is a statement about some entity. is our present definition. Helen Parkinson wrote: > information? > > Melanie Courtot wrote: >> Hi James, >> >> Thanks for the information, good to know it is all in progress :) >> >> I have added a tracker item for the Information Content Entity >> issue, at >> http://code.google.com/p/information-artifact-ontology/issues/detail?id=74 >> >> Do you have a definition/label to suggest that would be better for >> your users to get us started? >> >> Thanks, >> Melanie >> >> >> On 20-Jan-10, at 2:40 AM, James Malone wrote: >> >> >>> Sorry, I missed your part about "information content entity" as >>> well. I would love to pull in the metadata for this class too but >>> the definition "an information content entity is an entity that is >>> generically dependent on some artifact and stands in relation of >>> aboutness to some entity" is confusing for our users and curators. >>> Suffice to say, we mean the same thing as IAO mean by information >>> and we use the same URI to indicate this, but the definition and >>> label, less so. >>> >>> James >>> >>> >>> >>> >>> James Malone wrote: >>> >>>> Hi Melanie, >>>> >>>> Indeed it is work that is in the pipeline and something I am >>>> working on now. We will release a version in the near future where >>>> the relations and IAO/OBI classes use the same URIs. Part of the >>>> initial reason for ignoring of IAO and OBI/RO URIs is that they >>>> are not stable at the moment. I have specifically asked the RO >>>> people for details on when the URIs will be stable and the answer >>>> was they will change again in the near future - this is something >>>> we will have to deal with I think when it happens as I agree using >>>> the same relations is advantageous (and is our aim). I should also >>>> add we are looking to encourage people to contribute to the >>>> software ontology so if other users are interested we are happy to >>>> have them on board. >>>> >>>> James >>>> >>>> >>>> Melanie Courtot wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> I am subscribed to a mailing-list where a message was posted >>>>> this morning >>>>> (http://groups.google.com/group/resource-representation-coordination/msg/b205ebc91fc7458f >>>>> ) regarding relations and mireoting. >>>>> >>>>> Following that message I went to check the SWO file. >>>>> >>>>> I have a few questions, maybe you can help: >>>>> >>>>> 1. As Carlo mentions, the relations have new IDs >>>>> For example: >>>>> <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/swo/ >>>>> SWO_0000735"> >>>>> <rdfs:label rdf:datatype="http://www.w3.org/2001/ >>>>> XMLSchema#string">has_specified_output</rdfs:label> >>>>> </owl:ObjectProperty> >>>>> >>>>> I was wondering what prevented you from re-using directly the >>>>> OBI ones, you would 1/ keep the IDs 2/ avoid user confusion 3/ >>>>> get the definitions and domain/range for free >>>>> >>>>> 2. Similar question regarding is_about >>>>> <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/swo/ >>>>> SWO_0000732"> >>>>> <rdfs:domain >>>>> rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030 "/> >>>>> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >>>>> >>>>>> is about</rdfs:label> >>>>>> >>>>> </owl:ObjectProperty> >>>>> >>>>> It is even stranger as you re use the IAO class to define the >>>>> domain, so I am not sure why not push the reasoning all the way >>>>> and take directly the IAO relation? >>>>> >>>>> 3. Algorithm >>>>> >>>>> While browsing I noticed there are few classes that are redundant >>>>> with IAO. For example: >>>>> <owl:Class rdf:about="http://www.ebi.ac.uk/efo/swo/SWO_0000462"> >>>>> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >>>>> >>>>>> algorithm</rdfs:label> >>>>>> >>>>> <rdfs:subClassOf> >>>>> <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/> >>>>> </rdfs:subClassOf> >>>>> </owl:Class> >>>>> >>>>> Again, why not take directly the IAO class in, especially as you >>>>> assert it under an IAO class. >>>>> >>>>> 4. IAO_0000030 >>>>> <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"> >>>>> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >>>>> >>>>>> information</rdfs:label> >>>>>> >>>>> </owl:Class> >>>>> >>>>> I noticed that you just took in the label information, while the >>>>> class is actually called information content entity. Was there >>>>> any reason to relabel the class? I find that somehow disturbing, >>>>> especially as you didn't take in the definition. I'm wondering >>>>> if it may not lead to confusion/issues later on. >>>>> >>>>> Of course I understand that the resource is fairly new (I saw >>>>> only 2 releases on BioPortal), and that work is most probably >>>>> still in progress, so the above may already be planned for next >>>>> releases. >>>>> >>>>> Thanks, >>>>> Melanie >>>>> >>>>> >>>>> --- >>>>> Mélanie Courtot >>>>> TFL- BCCRC >>>>> 675 West 10th Avenue >>>>> Vancouver, BC >>>>> V5Z 1L3, Canada >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> Throughout its 18-year history, RSA Conference consistently >>>>> attracts the >>>>> world's best and brightest in the field, creating opportunities >>>>> for Conference >>>>> attendees to learn about information security's most important >>>>> issues through >>>>> interactions with peers, luminaries and emerging and established >>>>> companies. >>>>> http://p.sf.net/sfu/rsaconf-dev2dev >>>>> _______________________________________________ >>>>> EFO-users mailing list >>>>> EFO...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/efo-users >>>>> >>>>> >>>> >>>> >>> -- >>> European Bioinformatics Institute, Wellcome Trust Genome Campus, >>> Hinxton, Cambridge, CB10 1SD, United Kingdom >>> Tel: + 44 (0) 1223 494 676 >>> Fax: + 44 (0) 1223 492 468 >>> >> >> --- >> Mélanie Courtot >> TFL- BCCRC >> 675 West 10th Avenue >> Vancouver, BC >> V5Z 1L3, Canada >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Throughout its 18-year history, RSA Conference consistently attracts the >> world's best and brightest in the field, creating opportunities for >> Conference >> attendees to learn about information security's most important issues >> through >> interactions with peers, luminaries and emerging and established >> companies. >> http://p.sf.net/sfu/rsaconf-dev2dev >> _______________________________________________ >> EFO-users mailing list >> EFO...@li... >> https://lists.sourceforge.net/lists/listinfo/efo-users >> -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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