Latest revision as of 21:15, 11 April 2012

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG)

Collaborators: Mary Schaeffer, MaizeGDB

Streaming recording link

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:

- PO:0009066 anther: part_of(PO:0006310) (tassel floret; for anthers R1 B73 )

- PO:0009054 inflorescence bract: part_of(PO:0020136) (ear inflorescence; for husk, innermost R1 B73, husk, innermost R2 B73, and husk, outer R2 B73)

- PO:0006339 juvenile leaf: part_of(PO:0009025) (vascular leaf; for leaf 1st with sheath V3 B73)

- PO:0020040 leaf base: part_of(PO:0009025) (vascular leaf; for leaf base of expanding leaf V7 B7)

- PO:0006340 adult leaf: part_of(PO:0009025) (vascular leaf; for leaf, 13th V9 B73)

- PO:0009074 style: part_of(PO:0006354, or use PO:0006350, PO:0006351, PO:0006352 or PO:0006353 if appropriate) (for silks R1 B73)

(PO:0006354=ear floret; PO:0006350 =upper floret of pedicellate spikelet of ear; PO:0006351=lower floret of sessile spikelet of ear; PO:0006352=upper floret of sessile spikelet of ear; PO:0006353=lower floret of pedicellate spikelet of ear)

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 line script 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_genemodel__zea_MaizeGDB.assoc (use aspect A)

po_development_genemodel__zea_MaizeGDB.assoc (use aspect D)

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.

[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

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 to the tissue pages from there

Linking to the gene model pages:

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 (RW: see bottom link on the list below. This is the current link to the gene model pages. MS should confirm that this is stable.)

Dbxrefs file:

current contents

PO has two stanzas for MaizeGDB 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 contain multiple url syntaxes (is this allowed?) and do not provide examples.

proposed contents

Need to consult with Mary about what should link where.

Under construction

"canonical name of gene" and "Phenotype of gene variant":

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=

"locus identifier" and "phenotype identifier":

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=

gene model pages:

abbreviation: MaizeGDBID_genmod

database: Maize Genome Database

object: gene model name

example: MaizeGDBID_genmod:GRMZM2G172795

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=

url_example: http://http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G172795

tissue pages (if needed):

abbreviation: MaizeGDBID_termref

database: Maize Genome Database

object: tissue description

example: MaizeGDBID_termref:2366347

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=

url_example: http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347

Maize tissue Pages:

MGDB_tissue:2366347 anthers R1 B73

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: [1]

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. done

for:

new annotations
merged terms
obsoleted terms

These changes need to be made in the maizeGDB database as well, so they won't have to be updated every time MaizeGDB updates their files. In each case, the lines of the annotation file should be changed to the new PO term.

List of merged terms

Note that in some cases, there are two layers of merging, so, for example, the annotations for PO:0006472 Zea stamen and PO:0006441 Poaceae stamen both need to be transferred to PO:0009029 stamen.

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

Open Source Forge tracker items

MS: Could you please look at the following tracker items, and post a comment on them if you think there are any problems:

See also the PO responses on the tracker items for:

IL.03 full inflorescence length reached

LP.18 eighteen leaves visible

3 inflorescence visible

These are all ok, MS is fine with what we decided to do with them

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.

Difference between revisions of "Follow up meeting: Sept 15, 2011"

Latest revision as of 21:15, 11 April 2012

Contents

Formatting of Association Files

Links to the Zm GeneModels and tissue pages

Dbxrefs file:

current contents

proposed contents

Maize tissue Pages:

Merging all of the Zea/Poaceae terms into their parent terms

List of merged terms

Open Source Forge tracker items

Navigation menu

Page actions

Page actions

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IN DISCUSSION

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@@ Line 15: / Line 15: @@
 *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:
+**PO:0009066  anther: part_of(PO:0006310) (tassel floret; for anthers R1 B73 )
+**PO:0009054 inflorescence bract: part_of(PO:0020136) (ear inflorescence; for husk, innermost R1 B73, husk, innermost R2 B73, and husk, outer R2 B73)
+**PO:0006339 juvenile leaf: part_of(PO:0009025) (vascular leaf; for leaf 1st with sheath V3 B73)
+**PO:0020040 leaf base: part_of(PO:0009025) (vascular leaf; for leaf base of expanding leaf V7 B7)
+**PO:0006340 adult leaf: part_of(PO:0009025) (vascular leaf; for leaf, 13th V9 B73)
+**PO:0009074 style: part_of(PO:0006354, or use PO:0006350, PO:0006351, PO:0006352 or PO:0006353 if appropriate) (for silks R1 B73)
+''(PO:0006354=ear floret; PO:0006350 =upper floret of pedicellate spikelet of ear; PO:0006351=lower floret of sessile spikelet of ear; PO:0006352=upper floret of sessile spikelet of ear; PO:0006353=lower floret of pedicellate spikelet of ear)''
 * 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
@@ Line 20: / Line 35: @@
 ''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''
+''After the call: JE sent MS a command line script to remove the commas and replace with tabs''
 ''Should we add this on the Documentation Page as a general guideline?''
@@ Line 27: / Line 42: @@
 ''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
+* 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''
+''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_anatomy_genemodel__zea_MaizeGDB.assoc (use aspect A)
-po_development_gene_model__zea_MaizeGDB.assoc (use aspect D)
+po_development_genemodel__zea_MaizeGDB.assoc (use aspect D)
-*Linking to the GRMZM pages:
+=Links to the Zm GeneModels and tissue pages=
-Need to update the Dbxrefs see below
+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
-*Display of the Pubmed Publications:
+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''
-po_anatomy_gene_model__zea_MaizeGDB.assoc (use aspect A)
+*Display of the Pubmed Publications:
-po_development_gene_model__zea_MaizeGDB.assoc (use aspect D)
+''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 to the tissue pages from there''
-=Merging all of the Zea/Poaceae terms into their parent terms=
+*Linking to the gene model pages:
-Detailed all of the changes on our wiki page at: [[Eliminating_Zea/Poaceae_terms_from_PO]]
+''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'' (RW: see bottom link on the list below. This is the current link to the gene model pages. MS should confirm that this is stable.)
-=Open Source Forge tracker items=
+==Dbxrefs file:==
+===current contents===
-Could you please look at the following tracker items, and post a comment on them if you think there are any problems:
+PO has two stanzas for MaizeGDB in the dbxref file:
-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]]
+abbreviation: MaizeGDB
-glume: [[https://sourceforge.net/tracker/?group_id=76834&atid=835555]]
+database: Maize Genetics and Genome Database.
-floret: [[http://sourceforge.net/tracker/?func=detail&aid=3397632&group_id=76834&atid=835555]]
+object: Canonical name of gene.
+example: MaizeGDB:apb1
-I also posted our responses on your tracker items for:
+generic_url: http://www.maizegdb.org/
-IL.03 full inflorescence length reached: [[http://sourceforge.net/tracker/?func=detail&aid=3357762&group_id=76834&atid=835555]]
+url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=
-LP.18 eighteen leaves visible: [[https://sourceforge.net/tracker/?func=detail&aid=3357766&group_id=76834&atid=835555]]
+object: Phenotype of gene variant
-inflorescence visible  [[http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 inflorescence visible]
+example: MaizeGDB:liguleless
+url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term=
-coleoptile emergence
+abbreviation: MaizeGDBID
-=Links to the ZmGeneModels and tissue pages=
+database: Maize Genome Database.
-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.
+object: locus Identifier.
-[[http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G172795 GRMZM2G172795]]
+example: MaizeGDBID:12008
-From MS: What would be the best way to provide the maize tissue links?
+generic_url: http://www.maizegdb.org/
-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
-Else, for quicker lining with view of image and journal:  [[http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347 MGDB_tissue:2366347]]
+url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=
-Another way:
+object: phenotype identifier
-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''
+example:MaizeGDBID:61504
-''Need to figure out why the PubmedID is not showing up''
+url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id=
+''Note that both of these have a mistakes -- they contain multiple url syntaxes (is this allowed?) and do not provide examples.''
+===proposed contents===
+''Need to consult with Mary about what should link where.''
-'''dbxref urls:'''
+''Under construction''
-PO has two stanza in the dbxref file:
+'''"canonical name of gene" and "Phenotype of gene variant":'''
 abbreviation: MaizeGDB
@@ Line 112: / Line 142: @@
 url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=
 object: Phenotype of gene variant
@@ Line 119: / Line 151: @@
 url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term=
+'''"locus identifier" and "phenotype identifier":'''
 abbreviation: MaizeGDBID
@@ Line 131: / Line 165: @@
 url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=
 object: phenotype identifier
@@ Line 137: / Line 173: @@
 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)
+'''gene model pages:'''
+abbreviation: MaizeGDBID_genmod
+database: Maize Genome Database
+object: gene model name
+example: MaizeGDBID_genmod:GRMZM2G172795
+generic_url: http://www.maizegdb.org/
+url_syntax: http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=
+url_example: http://http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G172795
+'''tissue pages (if needed):'''
+abbreviation: MaizeGDBID_termref
+database: Maize Genome Database
+object: tissue description
+example: MaizeGDBID_termref:2366347
+generic_url: http://www.maizegdb.org/
+url_syntax: http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=
+url_example: http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347
+==Maize tissue Pages:==
+[http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347 MGDB_tissue:2366347 anthers R1 B73]
+''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. ''done''
+for:
+*new annotations
+*merged terms
+*obsoleted terms
+''These changes need to be made in the maizeGDB database as well, so they won't have to be updated every time MaizeGDB updates their files. In each case, the lines of the annotation file should be changed to the new PO term.''
-----
+==List of merged terms==
+''Note that in some cases, there are two layers of merging, so, for example, the annotations for PO:0006472 Zea stamen and PO:0006441 Poaceae stamen both need to be transferred to PO:0009029 stamen.''
-=List of merged terms=
 term (# annotations) > term merged into (= target term)
@@ Line 200: / Line 285: @@
 PO:0006450 Poaceae tapetum (3) > PO:0009071 anther wall tapetum
-PO:0006337 inflorescence bract of ear (26) > PO:0009054 inflorescence bract
+=Open Source Forge tracker items=
+MS: Could you please look at the following tracker items, and post a comment on them if you think there are any problems:
+[http://sourceforge.net/tracker/index.php?func=detail&aid=3132525&group_id=76834&atid=835555 Poaceae hull]
+[https://sourceforge.net/tracker/?func=detail&aid=3400245&group_id=76834&atid=835555 lemma/palea]
+[https://sourceforge.net/tracker/?group_id=76834&atid=835555 glume]
+[http://sourceforge.net/tracker/?func=detail&aid=3397632&group_id=76834&atid=835555 floret]
+See also the PO responses on the tracker items for:
+[http://sourceforge.net/tracker/?func=detail&aid=3357762&group_id=76834&atid=835555 IL.03 full inflorescence length reached]
+[https://sourceforge.net/tracker/?func=detail&aid=3357766&group_id=76834&atid=835555 LP.18 eighteen leaves 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.''