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POC members: Laurel Cooper (OSU), Ramona Walls (NYBG) Collaborators: Mary Schaeffer, MaizeGDB [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=57313312&rKey=d971eed7ec8daa24 Streaming recording link] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=57313312&rKey=178047667a7f37aa Download recording link] '''Items for discussion''' =Formatting of Association Files= *Question from MS @formatting column 16 correctly in last send - does it matter? You list on the po how to page an example: part_of(PO:0009025) ''The formatting for column 16 is correct'' *Adding the duplicate annotations for items also in column 16 will be done. Copy all the lines and replace the primary PO:ID with the one referred to in column 16. This will affect the following terms: (put in the list of terms) * A question about NULL values, may I use the term 'NULL'? Or do you require that there be a blank? These should be a hyphen ''The MaizeGDB files are built in their OracleDB then moved to Access, then to Excel. So it may have been an issue about crossing the software platforms. Mary will convert the Nulls to hyphens from the Oracle Tables. Their Databases are updated monthly. MS problem finding errors in perl. '' ''After the call: JE sent MS a command to remove the commas and replace with tabs'' ''Should we add this on the Documentation Page as a general guideline?'' *Request from MS: A tab-delimited file of all the 'obsolete' PO terms ''she does not need this anymore as the obsoleted terms now have 'obsolete' in the definition.'' * Test file on the SVN: po_anatomy_gene_zea_MaizeGDB_silk.assoc.txt ''MS will download it and check it and add the additional lines needed to refer to "part_of(PO:0006354), which is ear floret'' ''file will be saved as: po_anatomy_gene_zea_MaizeGDB_silk.assoc - to be consistent, don't need the .txt'' ''Once all the bugs are worked out of this file, the rest of the annotations will be submitted in two files: po_anatomy_gene_model__zea_MaizeGDB.assoc (use aspect A) po_development_gene_model__zea_MaizeGDB.assoc (use aspect D) =Open Source Forge tracker items= Could you please look at the following tracker items, and post a comment on them if you think there are any problems: Poaceae hull: [[http://sourceforge.net/tracker/index.php?func=detail&aid=3132525&group_id=76834&atid=835555]] lemma/palea: [[https://sourceforge.net/tracker/?func=detail&aid=3400245&group_id=76834&atid=835555]] glume: [[https://sourceforge.net/tracker/?group_id=76834&atid=835555]] floret: [[http://sourceforge.net/tracker/?func=detail&aid=3397632&group_id=76834&atid=835555]] I also posted our responses on your tracker items for: IL.03 full inflorescence length reached: [[http://sourceforge.net/tracker/?func=detail&aid=3357762&group_id=76834&atid=835555]] LP.18 eighteen leaves visible: [[https://sourceforge.net/tracker/?func=detail&aid=3357766&group_id=76834&atid=835555]] inflorescence visible [[http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 inflorescence visible]] ''These are all ok, MS is fine with what we decided to do with them'' [https://sourceforge.net/tracker/index.php?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence] ''MS says that the PO term radicle emergence is more applicable, so she will use that term, rather than coleoptile emergence. BTW: in corn seed the radicle emerges from the pericarp, rather than the seed coat.'' =Links to the Zm GeneModels and tissue pages= They will have same URL structure/link unless the models go away or change, and then it will be by synonym or something. They seem not to be changing too much between versions from the early reports - mostly coordinates. [[http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G172795 example: GRMZM2G172795]] From MS: What would be the best way to provide the maize tissue links? Can we use column 8 for example and supply in this form: MGDB_tissue:2366347, The URL would be the standard one for MaizeGDB – just by ID Another way: In the reference field, column 6, add the tissue ID (which links to the reference in the above link) - this is logically more consistent with GO notions I would think. ''Neither of these places in the annotation file will work. LC will create a page on our wiki with links to the tissue pages, and to a description of the experiments'' ''Need to figure out why the PubmedID is not showing up'' *Linking to the gene model pages: Need to update the Dbxrefs see below: ''The link in the "Assigned by" column should take you to the Gene model page. This is determined by the Dbxrefs file. Need to add an entry for the maize gene model name. MS will check with her person to find out how to link to these'' *Display of the Pubmed Publications: ''MS put in both the pubmed ID and the maizeGDB ID, as recommended, but only the maizeGDBID is showing up, but it is not creating a link there (check dbxrefs) and it is not displaying or linking to the pubmed citation. See what is up with this?'' ''If the maizeGDBID link was working it would link tot he tissue pages from there'' '''dbxref urls:''' PO has two stanza in the dbxref file: abbreviation: MaizeGDB database: Maize Genetics and Genome Database. object: Canonical name of gene. example: MaizeGDB:apb1 generic_url: http://www.maizegdb.org/ url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term= object: Phenotype of gene variant example: MaizeGDB:liguleless url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term= abbreviation: MaizeGDBID database: Maize Genome Database. object: locus Identifier. example: MaizeGDBID:12008 generic_url: http://www.maizegdb.org/ url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id= object: phenotype identifier example:MaizeGDBID:61504 url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id= ''Note that both of these have a mistakes -- they both have the same url syntax and an incorrect example of url syntax.'' The generic url for a gene model page is: http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id= ''We will need another stanza for this type of link (e.g., MaizeGDBgenemod)'' ==Maize tissue Pages:== [[http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347 MGDB_tissue:2366347]] ''MS will update the links on the tissue pages that refer to the PO terms and will link back to that page from the associated linked page: [http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=24749]'' ''LC will create a page on our wiki with links to the tissue pages, and to a description of the experiments'' =Merging all of the Zea/Poaceae terms into their parent terms= Detailed all of the changes on our wiki page at: [[Eliminating_Zea/Poaceae_terms_from_PO]] ''MS has already used the more general terms for these.'' *Updating the existing association files: MS will look after updating these files. LC will let JE know. for: *new annotations *merged terms *obsoleted terms ==List of merged terms== term (# annotations) > term merged into (= target term) PO:0006337 inflorescence bract of ear (26) > PO:0009054 inflorescence bract PO:0006472 Zea stamen (1) > PO:0006441 Poaceae stamen (7) > PO:0009029 stamen PO:0006473 Zea anther (363) > PO:0006442 Poaceae anther (6) > PO:0009066 anther PO:0006487 Zea stigma (56) > PO:0006468 Poaceae stigma (0) > PO:0009073 stigma PO:0006488 silk (56) > PO:0006469 Poaceae style (100) > PO:0009074 style PO:0006445 Poaceae anther wall (2) > PO:0000002 anther wall PO:0006455 Poaceae carpel (3) > PO:0009030 carpel PO:0006446 Poaceae endothecium (1) > PO:0020002 anther wall endothecium PO:0006318 Poaceae floret (71) > PO:0009082 floret PO:0006329 Poaceae floret meristem (1) > flower meristem PO:0000229 PO:0006384 Poaceae gynoecium (3) > PO:0009062 gynoecium PO:0006465 Poaceae integument (3) > PO:0020021 integument PO:0006508 Poaceae integument epidermis (1) > PO:0006043 integument epidermis PO:0006464 Poaceae megaspore (1) > PO:0020019 megaspore PO:0006463 Poaceae megasporocyte (2) > PO:0000431 megasporocyte PO:0006444 Poaceae microsporangium (2) > PO:0025202 microsporangium PO:0006452 Poaceae microspore (22) > PO:0020048 microspore PO:0006451 Poaceae microsporocyte (1) > PO:0020047 microsporocyte PO:0006462 Poaceae nucellus (2) > PO:0020020 nucellus PO:0006456 Poaceae ovary (1) > PO:0009072 ovary PO:0006457 Poaceae ovule (5) > PO:0020003 ovule PO:0006497 Poaceae stigma epidermis (3) > PO:0006061 stigma epidermis PO:0006449 Poaceae stomium (1) > PO:0020101 stomium PO:0006450 Poaceae tapetum (3) > PO:0009071 anther wall tapetum PO:0006337 inflorescence bract of ear (26) > PO:0009054 inflorescence bract

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