GPAD to .ace file

From WormBaseWiki
Jump to navigationJump to search

Back to Gene Ontology

This page outlines how we'll go forward with converting the gpad file we get back from UniProt into a .ace file for upload to citace.

The final file specifications for the GPAD file are available here:

http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format

Things to confirm:

  1. We get back from UniProt all C. elegans annotations, regardless of annotation source (e.g., WormBase, UniProt, IntAct, etc).
  2. We get back all data in the with/from column (e.g., variations, RNAi experiments)


A table mapping gpad columns to .ace:

gp_association files (GPAD)

N.B. The first line in the gp_association file should be;

!gpa-version: 1.1


Final format (09 Jan 2013)

column name required? cardinality old column # extra info .ace file equivalent how to populate
1 DB required 1 1 must be in xrf_abbs n/a n/a
2 DB_Object_ID required 1 2 canonical or spliceform ID Gene : "WBGene00000001" will need to map from UniProtKB IDs, using gp2protein file or later, gpi
3 Qualifier required 0 or greater 4 qualifiers to be confirmed n/a skip lines that have qualifiers
4 GO ID required 1 5 must be extant GO ID GO_term "GO:0008340" can take directly from file
5 DB:Reference(s) required 1 or greater 6 DB must be in xrf_abbs Paper_evidence "WBPaper00005614" We may need to map PMIDs or dois to WBPaper IDs
6 Evidence code required 1 7 from ECO "IMP" We may need to map ECO codes to three-letter abbreviations; would be good to ECO in WB
7 With (or) From optional 0 or greater 8 n/a n/a
8 Interacting taxon ID (for multi-organism processes) optional 0 or 1 13 NCBI taxon ID n/a n/a
9 Date required 1 14 YYYYMMDD Date_last_updated evidence can take directly from file
10 Assigned_by required 1 15 from xrf_abbs Curator_confirmed If WB, take value from Annotation Properties, if not WB, then we will need to create Person objects for other databases, e.g. UniProt, IntAct, PAINT (?)
11 Annotation Extension optional 0 or greater 16
12 Annotation Properties optional 0 or greater See Note 1 below

Notes

1. The Annotation Properties column can be filled with a pipe separated list of "property_name = property_value". There will be a fixed vocabulary for the property names and this list can be extended when necessary. The initial supported properties would be curator_name and annotation_identifier*, but can be extended to include e.g. curator_ID, modification_date, creation_date, annotation_notes...etc.

* curator_name and annotation_identifier will be useful for groups that are using Protein2GO for protein annotation who wish to maintain their annotations in their own database. These values can be used to keep track of individual annotations.

Further questions/discussion points

1. Qualifiers column. a. Are the explicit relations mandatory? b. If so, what are they.

2. Evidence column. a. Chain of evidence

3. Annotation properties column. Tony has suggested including the GO evidence code here to avoid using a lookup to reverse engineer the file