Difference between revisions of "OA and scripts for disease data"
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Similar to: WBGene in the GO OA or concise descrips OA <br/ > | Similar to: WBGene in the GO OA or concise descrips OA <br/ > | ||
As one starts typing locus name, eg, lin-10 or cosmid name, eg., C09H6 script autocompletes and fills in WBGene ID. <br/ > | As one starts typing locus name, eg, lin-10 or cosmid name, eg., C09H6 script autocompletes and fills in WBGene ID. <br/ > | ||
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| + | Q: So single value, not multiple ? | ||
| + | |||
'''Field 2 Name:''' Experimental model for <br/ > | '''Field 2 Name:''' Experimental model for <br/ > | ||
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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. <br/ > | 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. <br/ > | ||
Updating: How do we update this obo file, how frequently do other obo files get updated? <br/ > | Updating: How do we update this obo file, how frequently do other obo files get updated? <br/ > | ||
| + | |||
| + | Q: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 ? | ||
| + | |||
'''Field 3 Name:''' Paper for Experimental Model <br/ > | '''Field 3 Name:''' Paper for Experimental Model <br/ > | ||
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Obo file to be used: WBPaper obo <br/ > | Obo file to be used: WBPaper obo <br/ > | ||
Similar to: The Paper field in the GO OA | 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 <br/ > | '''Field 4 Name:''' Species <br/ > | ||
Revision as of 19:43, 11 January 2013
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 ?
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.
Updating: How do we update this obo file, how frequently do other obo files get updated?
Q: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 ?
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
Field 5 Name: xref Database
Behavior: Free text, multiple values comma-separated
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.
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
Field 8 Name: Database
Behavior: Free text, multiple values comma-separated
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
