OA and scripts for disease data

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Revision as of 20:01, 11 January 2013 by Rkishore (talk | contribs)
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OA for disease data in WormBase:

Editor:

Field 1 Name: WBGene
Behavior of field: Autocomplete obo
Source: WBGene obo
Similar to: WBGene in the GO OA or concise descrips OA
As one starts typing locus name, eg, lin-10 or cosmid name, eg., C09H6 script autocompletes and fills in WBGene ID.

Q: So single value, not multiple?
A: Single value.

Field 2 Name: Experimental model for
Behavior:Autocomplete obo
Obo file to be used: DO_term obo
Source: https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo
Similar to: GO term field in the GO OA.
For example, curator starts typing 'Alz', picks 'Alzheimer's disease' from the drop-down and script populates field with 'Alzheimer's disease (DOID:10652); similar to GO term OA in the GO OA.

Q:Updating: How do we update this obo file, how frequently do other obo files get updated?
A: Everyday at 8pm, if it has the proper .obo format it should be easy to add to the cronjob that picks them up.
/home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl

Q:Single value / multivalue ? A:

Field 3 Name: Paper for Experimental Model
Obo file to be used: DO_term obo
Behavior:Autocomplete obo
Obo file to be used: WBPaper obo
Similar to: The Paper field in the GO OA Q: You mean the papers in the paper editor ? Q:Single/multi ?


Field 4 Name: Species
Behavior: Auto-complete drop-down with ready values
Similar to: Project field in the GO OA
Current values: Homo sapiens

Q:Do you want to use the same list as everyone else, and add new values to it (if they're okay with those values) ?

Field 5 Name: xref Database
Behavior: Free text, multiple values comma-separated Q: Will they dump in separate lines in the output ? Usually those are pipe-separated. If they'll dump literally as pasted in, then commas are good.

Field 6 Name: Disease_relevance
Behavior: Big Text box (big text-box, keeps expanding)
Similar To: 'Description Text' field in the Concise OA.
This is the Human_disease_relevance description (it appears as one of the drop-down values) for the'Description Type' field in the 'Concise' OA.
Change needed: Human_disease_relevance will not be entered via the concise OA. We can remove the 'Human_disease_relevance' from the 'Description Type' field in the OA.
Q: So we remove it from the GO OA (?) Do we start this OA by populating it from existing data in the GO OA ? If so, let me know how to transfer the data.

Field 7 Name: Paper for Disease Relevance
Behavior: Autocomplete obo
Obo file to be used: WBPaper obo
Similar to: The Paper field in the GO OA

Q:So there's two papers fields. Are they both required, or it must have at least one, or nothing is required ? single/multi value ?

Field 8 Name: Database
Behavior: Free text, multiple values comma-separated
Same as xref Database, but a different field ?

It would probably be better if the labels were shorter (particularly 3 and 7), the labels in the editor have to match the column labels in data table.

Fields 1-5 will have a data-table associated with them, similar to the GO OA.
Data Table Columns:
WBGene
Experimental Model For
Paper
Species
xref Database