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Re: [Chebi-ontology] groups vs molecular entities - sequence ontology use case
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From: Colin B. <Bat...@rs...> - 2014-03-25 18:40:17
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Hello Matt and Mike, Good to hear there's some movement on the SO/ChEBI front! A while ago (oh my goodness it was November 2008 so in fact five and a half years ago) I consulted with the ChEBI team about a similar problem, that of rotaxanes and catenanes, which are covalently-connected systems that are mechanically interlocked. As a result they acquired the parent CHEBI:50959, mechanically-interlocked molecular entity, which is a child of CHEBI:50967, non-covalently-bound molecular entity. The other children of that at present are CHEBI:50968, pseudorotaxane (like a rotaxane, except the ring can come off the shaft), and CHEBI:39022, inclusion compound. I reckon dsDNA would sit best as a descendant of CHEBI:50967. Hope this is helpful (and doesn't directly contradict anything the ChEBI curators are about to say), Best wishes, Colin. -----Original Message----- From: che...@li... [mailto:che...@li...] Sent: 24 March 2014 09:29 To: che...@li... Subject: Chebi-ontology Digest, Vol 31, Issue 1 Send Chebi-ontology mailing list submissions to che...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/chebi-ontology or, via email, send a message with subject or body 'help' to che...@li... You can reach the person managing the list at che...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of Chebi-ontology digest..." Today's Topics: 1. difference generic sql dump 3_star allstar (Christoph Wiemers) 2. Re: EBI HELP: ChEBI (Janna Hastings) 3. Re: EBI HELP: ChEBI (Christoph Wiemers) 4. Data Relation (Christoph Wiemers) 5. ChEBI 3rd User Group Workshop, 25-26 March 2014 (Janna Hastings) 6. groups vs molecular entities - seqeunce ontology use case (Matthew Brush) ---------------------------------------------------------------------- Message: 1 Date: Fri, 19 Oct 2012 08:18:46 +0000 From: Christoph Wiemers <Chr...@in...> Subject: [Chebi-ontology] difference generic sql dump 3_star allstar To: "che...@li..." <che...@li...> Message-ID: <8DB...@in...> Content-Type: text/plain; charset="us-ascii" Hi all, i have a question regarding the generic sql dumps. What is the difference between 3_star and all_star? Cheers, Christoph Wiemers ------------------------------ Message: 2 Date: Fri, 19 Oct 2012 09:42:48 +0100 From: "Janna Hastings" <has...@eb...> Subject: Re: [Chebi-ontology] EBI HELP: ChEBI To: <chr...@in...>, <che...@eb...> Cc: che...@li... Message-ID: <004001cdadd5$b7846980$268d3c80$@ebi.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear Christoph, The 3_star dump file includes exclusively those compounds that our curators have fully annotated and checked all details. This is a somewhat smaller set of data compared to the all_star which includes additional "preliminary" entries that are in the database but still await manual checking. Best wishes, Janna -----Original Message----- From: che...@eb... [mailto:che...@eb...] On Behalf Of chr...@in... Sent: 19 October 2012 08:50 To: che...@eb... Subject: EBI HELP: ChEBI Hi, i have a question regarding the ChEBI generic SQL format. What is the difference between the all_star and 3_star dump? Kind Regards, Christoph Wiemers _______________________________________________ chebi-help mailing list che...@eb... http://listserver.ebi.ac.uk/mailman/listinfo/chebi-help ------------------------------ Message: 3 Date: Fri, 19 Oct 2012 09:05:24 +0000 From: Christoph Wiemers <Chr...@in...> Subject: Re: [Chebi-ontology] EBI HELP: ChEBI To: "che...@li..." <che...@li...> Message-ID: <D56...@in...> Content-Type: text/plain; charset="us-ascii" Dear Janna, thanks for the answer. I found two names.sql files in the ftp directory. ftp://ftp.ebi.ac.uk/pub/databases/chebi/generic_dumps Can you also tell me the difference between the names.sql from the generic_dumps directory and the names.sql.gz which is part of generic_dump_3star.zip ? Which one do i have to import into my database and in which order? Best wishes, Christoph > Dear Christoph, > > The 3_star dump file includes exclusively those compounds that our > curators have fully annotated and checked all details. This is a > somewhat smaller set of data compared to the all_star which includes additional "preliminary" > entries that are in the database but still await manual checking. > > Best wishes, > Janna > > -----Original Message----- > From: che...@eb... > [mailto:che...@eb...] On Behalf Of > chr...@in... > Sent: 19 October 2012 08:50 > To: che...@eb... > Subject: EBI HELP: ChEBI > > Hi, > > i have a question regarding the ChEBI generic SQL format. > > What is the difference between the all_star and 3_star dump? > > Kind Regards, > > Christoph Wiemers > _______________________________________________ > chebi-help mailing list > che...@eb... > http://listserver.ebi.ac.uk/mailman/listinfo/chebi-help > ------------------------------ Message: 4 Date: Wed, 21 Nov 2012 08:58:45 +0000 From: Christoph Wiemers <Chr...@in...> Subject: [Chebi-ontology] Data Relation To: "che...@li..." <che...@li...> Message-ID: <AA9...@IQ...> Content-Type: text/plain; charset="us-ascii" Hi, i have compared the chebie.owl file with the database and the ontology lookup service on chebis website. http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CHEBI I see some difference in the data. Maybe somebody can help me. My starting point in the hierarchy is 'atom' CHEBI 33250. The ontology lookup service is telling me that atom has four child nodes ("main goup element atom", "metal atom", "nonmetal atom", "s-block element atom"). When i look into the 3_star chebi database i only get two of the four child nodes. My Query is: SELECT source_com.id AS node, dest_com.id AS narrower FROM compounds AS source_com JOIN vertice AS source_vertice ON source_com.id = source_vertice.compound_id JOIN relation AS source_relation ON source_relation.init_id = source_vertice.id JOIN vertice AS dest_vertice ON source_relation.final_id = dest_vertice.id JOIN compounds AS dest_com ON dest_vertice.compound_id = dest_com.id WHERE source_com.id='33250' AND source_relation.type = 'is_a' ORDER BY narrower; Maybe i am doing something wrong here? Kind regards, Christoph Wiemers ------------------------------ Message: 5 Date: Thu, 16 Jan 2014 14:32:00 -0000 From: "Janna Hastings" <has...@eb...> Subject: [Chebi-ontology] ChEBI 3rd User Group Workshop, 25-26 March 2014 To: <che...@li...> Message-ID: <001801cf12c7$b76f72c0$264e5840$@ebi.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear all, (with apologies for cross-posting) We are pleased to announce ChEBI's 3rd User Group Workshop being held at the EBI site in Hinxton, UK, on the 25th and 26th March 2014. The purpose of the workshop will be to explore recent enhancements and proposed new developments, with a specific focus on ChEBI's usability for the systems biology and metabolic modelling communities. For more information and a detailed schedule, please see the workshop website: http://www.ebi.ac.uk/training/course/chebi2014. All are welcome but attendance is limited - places will be allocated on a first come, first served basis. To register, please email Janna Hastings or Neil Swainston before the 20th February, 2014 (has...@eb... / nei...@ma...). Best wishes, Janna ---------------------------------------------------------------------------- ---------------------------------- Janna Hastings Email: has...@eb... | Tel: +44 (0)1223 494411 | Fax: +44 (0)1223 494468 Twitter: @jannahastings | Web: www.ebi.ac.uk/~hastings | Blog: www.bioontology.ch <http://www.bioontology.ch/> Coordinator, Cheminformatics and Metabolism, European Bioinformatics Institute ---------------------------------------------------------------------------- ---------------------------------- Visit ChEBI at www.ebi.ac.uk/chebi -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 6 Date: Sat, 22 Mar 2014 00:04:39 +0000 From: Matthew Brush <br...@oh...> Subject: [Chebi-ontology] groups vs molecular entities - seqeunce ontology use case To: "che...@li..." <che...@li...> Cc: Melissa Haendel <ha...@oh...>, "Bada, Mike \(Mik...@uc...\)" <Mik...@uc...> Message-ID: <04E...@EX...> Content-Type: text/plain; charset="us-ascii" Hi all, The developers of the Sequence Ontology are currently building a Molecular Sequence Ontology (MSO), which will represent sequence macromolecules and their parts. This is meant to parallel the existing abstract/GDC-level content of the SO. We are aiming to align the MSO with ChEBI in the interest of data interoperability, and will likely have some questions and feedback over the coming months in this regard. At the present time, we have some pressing questions concerning the nature of ChEBI:molecular entities and ChEBI:groups as they relate to sequence macromolecules and their parts. ChEBI definitions for these terms are below: molecular entity - any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity groups - a defined linked collection of atoms or a single atom within a molecular entity At issue for us is how to classify non-covalently associated components molecular complexes or ion pairs with respect to being 'molecular entities' or 'groups' (e.g. a single strand of a dsDNA macromolecule, a peptide subunit of a protein complex, or a hydroxide ion in a bonded NaOH ion pair). For molecular entities, what does "identifiable as a separately distinguishable entity" mean? It's clear that this excludes a subset of connected atoms that are covalently linked with other atoms to form a larger structure. However, it doesn't seem to exclude all proper parts of molecular entities; for example, all ions are categorized as molecular entities, yet ions can obviously associate with other ions into larger structures. Is a chemical entity "identifiable as a separately distinguishable entity" only if it is not covalently connected with other atoms forming a larger structure? Or is a non-covalently associated component of a molecular entity/complex also considered separately distinguishable? Is it possible that such an entity could qualify as both a molecular entity and a group (we noted that molecular entity and group are not asserted as disjoint)? Conversely, for groups, does "linked collection" refer to a continuous covalently linked collection of atoms? And does "within a molecular entity" necessarily refer to a subset of atoms that are covalently continuous with all other atoms? The exemplar use case we are facing for the MSO is in defining a 'base-paired DNA strand' class, which represents a single DNA chain that's part of a double-stranded DNA macromolecule. According to the ChEBI definitions above it would seem to qualify as a ChEBI:group (it is a "defined linked collection of atoms within a (dsDNA) molecular entity"). But if a DNA strand would also be considered "separately distinguishable", it would also seem to qualify as a molecular entity. Any clarifications and thoughts on the example above and the general questions it raises would be helpful. Thanks! Matthew Brush and Mike Bada ------------------- Matthew H. Brush Senior Research Associate OHSU Ontology Development Group Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University phone : 919-452-6914 fax : 503-346-6815 br...@oh... -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. 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