https://wiki.geneontology.org/index.php?title=SWUG:Meeting_at_Stanford_2011_06_23&feed=atom&action=historySWUG:Meeting at Stanford 2011 06 23 - Revision history2024-03-28T21:51:52ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=SWUG:Meeting_at_Stanford_2011_06_23&diff=53755&oldid=prevGail at 22:07, 14 July 20142014-07-14T22:07:34Z<p></p>
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</table>Gailhttps://wiki.geneontology.org/index.php?title=SWUG:Meeting_at_Stanford_2011_06_23&diff=36127&oldid=prevHitz: Created page with "* Waiting for The Mungall * Intro - new database "GOLD" ** VARCHARs used instead of incrementing primary key ** ontology schema updated to emulate OWL (not exactly a mirror) ** s..."2011-06-23T19:28:38Z<p>Created page with "* Waiting for The Mungall * Intro - new database "GOLD" ** VARCHARs used instead of incrementing primary key ** ontology schema updated to emulate OWL (not exactly a mirror) ** s..."</p>
<p><b>New page</b></p><div>* Waiting for The Mungall<br />
* Intro - new database "GOLD"<br />
** VARCHARs used instead of incrementing primary key<br />
** ontology schema updated to emulate OWL (not exactly a mirror)<br />
** schema designed to mirror GAF table "simpler", not as normalized<br />
*** actually "GPAD" format "Gene Product Annotation Data" (i.e, GAF sans Gene Product info<br />
*** files can be dealt with independently<br />
** No diagram yet ACTION ITEM: Make ERD -- Amelia<br />
** 3 modules in DB<br />
*** Ontology - more tables than old, less generic. View for inferred relationships.<br />
*** Association<br />
*** Phylogeny (in Grant, sorta nascent)<br />
** Other ontologies don't use always use RDB - "RDF triple store" ACTION ITEM: If you don't know what that is, google it.<br />
* Middleware<br />
** Replace go-db-perl and various friends with Java/Hibernate based ORM. <br />
** Some functions are hibernate independent - bulk-loader PG loader of tab-delimited files<br />
** Incremental update "delta" - script to create "delta files" and runs a hibernate script to do CRUD.<br />
** works for both Ontology and Annotation<br />
** "Deltas" are actually stored in DB.<br />
** API can be accessed via command-line scripts or Java servlet interface. Possibly expanded into WebServices<br />
** Bundled quality control scripts<br />
*** ontology GC (downstream of OBO-Edit)<br />
*** annotation filtering script - some rules hard coded but others are in a QC XML file<br />
** Files could be submitted by groups and run through QC pipeline<br />
** QC Web Interface can be used instead of or in addition to flat file management system "CVS"<br />
** Switching cost to remove CVS? Possible bridging software.<br />
** Could be done prior to full LEAD->GOLD switchover<br />
** Issues with non-up-to-date Ontology files, obsolete terms<br />
** Should we make hard QC checks really hard? How to enforce compliance?<br />
** Non-compliant evidence code flag? Shows up in AmiGO?<br />
* Progress Report(s)<br />
** Seth - SOLR/Lucene (future of AmiGO)<br />
*** Replace all go-perl/go-db-perl with SOLR/Lucene<br />
*** Create lucene indexes from GOLD (parallel processing)<br />
*** will be very fast once indexes are built<br />
*** could have additional "full searches" hooked up to DB<br />
*** similar to quickGO - dumped custom indexing at EBI<br />
*** where do the webservers go?<br />
*** what machines do we need? Probably at least as much<br />
*** lucene can help GoTermFinder with term look ups, Transitive Closure can be stored in memory<br />
** Shahid - infrastructure<br />
*** see above<br />
** Craig - update at Stanford<br />
*** have "genome-psquele" machine set up, PG set up. Software installed.<br />
*** Works, not sure what do load etc.<br />
** Kalpana - GoMine<br />
*** using InterMine datawarehouse <br />
*** ontology and annotation files loaded.<br />
*** working on loading uniprot (shahid has a splitter for this issue)<br />
*** issues with loading many taxa, id mapping<br />
* Future plans<br />
** Roadmap for upgrade<br />
*** Minimum functionality needed for clean break - deadline next GO meeting (Nov 7)<br />
**** Amigo2 in beta (includes GOOSE) <br />
**** GOLD feature complete <br />
**** OBOGalaxy released<br />
**** PAINT upgraded to use GOLD<br />
**** Testing env set up at Stanford<br />
** Hardware architecture things<br />
*** need proposal based on loading times (end August?)<br />
*** front end machines (Amigo, GOOSE, annotation QC), SOLR machines, Indexing machines, GOLD machines<br />
*** virtualization? (BB used xen, but now KVM: more stable, fewer features)<br />
**** mostly Ubuntu and Debian.<br />
**** libvirt python interface<br />
**** bad hardware is bad<br />
* Demo<br />
* Other projects<br />
** PAINT <br />
*** connects to LEAD schema using Hibernate; can be converted to GOLD one presumes<br />
*** ACTION ITEM: find someone to do this and find how long (Chris)<br />
** TermGenie<br />
*** Uses OWL API to get instantaneous terms requests. runs off a jetty server<br />
*** needs persistence layer to track</div>Hitz