From tberardi at acoma.stanford.edu Wed Aug 13 10:37:03 2008 From: tberardi at acoma.stanford.edu (Tanya Berardini) Date: Wed, 13 Aug 2008 10:37:03 -0700 Subject: [Gofriends] Additional inter- and intra-ontology 'regulates' links in the GO coming Message-ID: <8e22ab960808131037m6b9566e5qbb311b8fe3b41ff4@mail.gmail.com> Dear GO Friends, Having successfully implemented the 'regulates' relationships in the biological process (BP) ontology, we now plan to add 'regulates' relationships within the molecular function (MF) ontology and between the BP and MF ontologies. The target date for these additions is February 9, 2009. These additions may have great impact on your tools and analyses because: 1. There will be inter-ontology links between BP and MF for the first time. 2. Loading scripts will need to be modified to take the inter-ontology links into account by Feb. 9, 2009. 3. GO analysis tools will need to be modified to take the new relationships into account by Feb. 9, 2009. -- Specifically, we will make the implicit regulatory relationships between 'regulation of molecular function' BP terms and the corresponding MF terms explicit. For example: - regulation of kinase activity (BP) *regulates* kinase activity (MF) Similarly, we will make the implicit regulatory relationships between terms within the MF ontology explicit. For example: - calcium channel regulator activity (MF) *regulates* calcium channel activity (MF) The former will be the first inter-ontology links in the GO vocabularies. Note that if software has been constructed with the assumption that there are no inter-ontology links, then this software may break when presented with the new ontology. Adding these relationships improves the ability of the ontology to represent biology completely and accurately. The average GO user will benefit from these new links because they will be able to ask and answer more complex questions than they could previously. Users must understand what the different relationships mean and how the various GO tools utilize them. The addition of these links also has major implications for tools that ignore relationship types when summarizing annotations. For example, it is important to understand whether a query will return all children of a term regardless of its relationship to the parent, or can discriminate between relationship types. If your tool of choice lumps annotations to 'calcium channel regulator activity' together with the regulates parent 'calcium channel activity', a query for calcium channels will also retrieve gene products that function as calcium channel regulators (and not necessarily as channels!). More sophisticated tools will allow users to customize queries to return results that better reflect their interests. For example, tools that are upgraded to take relationships into consideration will allow users to look for processes or functions, and specify whether to include or exclude their regulates children. A test file with the BP-MF links can be found in the GO scratch directory: http://www.geneontology.org/scratch/regulates_relations_examples/go_regtest_withPosNeg_withPF_noXP.obo We will provide a test file with both BP-MF and MF-MF shortly. As noted, we plan to implement these links in the live ontology on February 9, 2009. Please provide feedback to us regarding this plan. We have created a wiki page http://wiki.geneontology.org/index.php/FP-regulates which will provide a more formal specification for software developers and database administrators. It will also provide answers to frequently asked questions and will be kept up to date with our progress. On behalf of the GO Consortium, Tanya Berardini David Hill Chris Mungall -------------- next part -------------- An HTML attachment was scrubbed... URL: From alanruttenberg at gmail.com Wed Aug 13 23:15:15 2008 From: alanruttenberg at gmail.com (Alan Ruttenberg) Date: Thu, 14 Aug 2008 02:15:15 -0400 Subject: [Gofriends] Additional inter- and intra-ontology 'regulates' links in the GO coming In-Reply-To: <8e22ab960808131037m6b9566e5qbb311b8fe3b41ff4@mail.gmail.com> References: <8e22ab960808131037m6b9566e5qbb311b8fe3b41ff4@mail.gmail.com> Message-ID: <06A25808-D0DD-45EB-A9B1-F31DD474B253@gmail.com> Can we have a definition of "regulates" please, that allows it to be the case that a function is regulated? Thanks, Alan On Aug 13, 2008, at 1:37 PM, Tanya Berardini wrote: > Dear GO Friends, > > Having successfully implemented the 'regulates' relationships in > the biological process (BP) ontology, we now plan to add > 'regulates' relationships within the molecular function (MF) > ontology and between the BP and MF ontologies. The target date for > these additions is February 9, 2009. > > These additions may have great impact on your tools and analyses > because: > > There will be inter-ontology links between BP and MF for the first > time. > Loading scripts will need to be modified to take the inter-ontology > links into account by Feb. 9, 2009. > GO analysis tools will need to be modified to take the new > relationships into account by Feb. 9, 2009. > -- > > Specifically, we will make the implicit regulatory relationships > between 'regulation of molecular function' BP terms and the > corresponding MF terms explicit. For example: > > regulation of kinase activity (BP) regulates kinase activity (MF) > Similarly, we will make the implicit regulatory relationships > between terms within the MF ontology explicit. For example: > > calcium channel regulator activity (MF) regulates calcium channel > activity (MF) > The former will be the first inter-ontology links in the GO > vocabularies. Note that if software has been constructed with the > assumption that there are no inter-ontology links, then this > software may break when presented with the new ontology. > > Adding these relationships improves the ability of the ontology to > represent biology completely and accurately. The average GO user > will benefit from these new links because they will be able to ask > and answer more complex questions than they could previously. Users > must understand what the different relationships mean and how the > various GO tools utilize them. > > The addition of these links also has major implications for tools > that ignore relationship types when summarizing annotations. For > example, it is important to understand whether a query will return > all children of a term regardless of its relationship to the > parent, or can discriminate between relationship types. If your > tool of choice lumps annotations to 'calcium channel regulator > activity' together with the regulates parent 'calcium channel > activity', a query for calcium channels will also retrieve gene > products that function as calcium channel regulators (and not > necessarily as channels!). More sophisticated tools will allow > users to customize queries to return results that better reflect > their interests. For example, tools that are upgraded to take > relationships into consideration will allow users to look for > processes or functions, and specify whether to include or exclude > their regulates children. > > A test file with the BP-MF links can be found in the GO scratch > directory: > > http://www.geneontology.org/scratch/regulates_relations_examples/ > go_regtest_withPosNeg_withPF_noXP.obo > We will provide a test file with both BP-MF and MF-MF shortly. > > As noted, we plan to implement these links in the live ontology on > February 9, 2009. > > Please provide feedback to us regarding this plan. We have created > a wiki page > > http://wiki.geneontology.org/index.php/FP-regulates > which will provide a more formal specification for software > developers and database administrators. It will also provide > answers to frequently asked questions and will be kept up to date > with our progress. > > On behalf of the GO Consortium, > > Tanya Berardini > > David Hill > > Chris Mungall > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends -------------- next part -------------- An HTML attachment was scrubbed... URL: From aji at ebi.ac.uk Tue Aug 26 13:19:36 2008 From: aji at ebi.ac.uk (Amelia Ireland) Date: Tue, 26 Aug 2008 13:19:36 -0700 Subject: [Gofriends] August 2008 newsletter Message-ID: <3F7ABEBA-94FC-478D-A40E-CFEDB0B97646@ebi.ac.uk> Dear friends of the GO project, It gives me great pleasure to report that the August 2008 Gene Ontology newsletter is now out! This issue covers the following topics: - Genes of the Quarter: Excision-Repair Proteins - Resource List: ID Mapping - Announcements -> Dual Taxon Annotations Now in the GO Association Files -> Process-Function Relationships -> JCVI Eukaryotic Genome Annotation and Analysis Course - Upcoming Events The full text of the newsletter can be viewed online: HTML - http://www.geneontology.org/newsletter/current-newsletter.shtml PDF - http://www.geneontology.org/newsletter/current-newsletter.pdf Enjoy! Thanks, The GO newsletter team. -- Amelia Ireland GO Editorial Office http://www.ebi.ac.uk || http://www.berkeleybop.org BBOP Plant Project: http://bbopgarden.blogspot.com