OA and scripts for disease data

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OA for disease data in WormBase


Field 1 Name: dis_wbgene 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: dis_curator Curator
Behavior of field: Auto-complete drop-down with ready values
Similar to: Curator field in GO OA

Field 3 Name: dis_curhistory Curator History Behavior of field: However it is in the concise OA; this is not something that can be changed manually.
Similar to: consise OA

Field 4 Name: dis_expmodelfor 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.

Q: Single value / multivalue ?
A: Multiple value, as I may need to attach more than one DO term to a gene.

Field 5 Name: dis_paperexpmod Paper for Exp Mod
Obo file to be used: Paper 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 ?
The Paper obo, I guess they all come from the Paper Editor.

Q:Single/multi ?
Multi value.

Field 6 Name: dis_species 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) ?
A: Yes, I just spoke to Daniela and adding the value 'Homo sapiens' is fine with her, if you want I can e-mail the group, but she felt adding needed values was fine.

Field 7 Name: dis_xrefdb 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.
A: Per latest conversation, using commas is fine, as long as there never will be a comma in the data itself, which is not likely to happen as these are OMIM IDs

Field 8 Name: dis_diseaserelevance 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:Do we start this OA by populating it from existing data in the GO OA ?
A:You mean 'existing data in the concise description OA, We can, if thats the way you want to start, or we can do it later.

Q: If so, let me know how to transfer the data.
A: So for any given 'Human disease relevance' description in the concise OA the transfer from Concise OA to Gene-disease OA is as follows:
Curator History-->Curator History
Description Text (Human Disease Relevance)-->Disease Relevance
Reference-->Reference under Disease Relevance
Accession Evidence-->OMIM Database
Last Updated-->Last updated PGID-->PGID

Field 9 Name: dis_paperdisrel Paper for Disease Rel
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 ?
A: Both are required.
Q:single/multi value ?
A: Multivalue

Field 10 Name: dis_omimdb OMIM Database
Behavior: Free text, multiple values comma-separated

Q:Same as xref Database, but a different field ?
A: Exactly, again I will pipe-separate multiple values.

Field 11 Name: dis_lastupdate Last Updated
Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD

Field 12 Name: dis_comment Comment
Behavior: Free text

Field 13 Name: pgid

Data constraints

For curators only at the tool level to check if required fields are filled.
Experimental model for
Paper for Exp Mod
Disease relevance
Paper for Disease Rel
Last Updated

To make live:
at : /home/postgres/work/pgpopulation/dis_disease/
create_dis_tables.pl -- create new postgres tables for dis_ disease OA
synchronize OA
transfer_concise_disease.pl -- take 95 entries that have con_desctype = 'Human_disease_relevance' and add them to dis_ tables starting with pgid 1.
Ranjana, manually delete the Human_disease_relevance entries from the concise OA.
remove the Human_disease_relevance option from the OA, resynchronize.

Changes needed 1/14/13:
  • Separate 'Last Updated field' for Experimental Model for section of the data, so would be Field 8.
Dumper specifications


DB_info  Database ?Database ?Database_field Text
Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species   #Evidence	            
             Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence
             Disease_relevance  ?Text ?Species #Evidence