Difference between revisions of "OA and scripts for disease data"

From WormBaseWiki
Jump to navigationJump to search
Line 12: Line 12:
 
A: Single value. <br/ >
 
A: Single value. <br/ >
  
'''Field 2 Name:''' Experimental model for <br/ >
+
'''Field 2 Name:''' Curator
 +
Behavior of field: Auto-complete drop-down with ready values
 +
Similar to: Curator field in GO OA
 +
 
 +
 
 +
'''Field 3 Name:''' Experimental model for <br/ >
 
Behavior:Autocomplete obo <br/ >  
 
Behavior:Autocomplete obo <br/ >  
 
Obo file to be used: DO_term obo <br/ >  
 
Obo file to be used: DO_term obo <br/ >  
Line 27: Line 32:
 
A: Multiple value, as I may need to attach more than one DO term to a gene.
 
A: Multiple value, as I may need to attach more than one DO term to a gene.
  
'''Field 3 Name:''' Paper for Experimental Model (Call it just Paper) <br/ >  
+
'''Field 4 Name:''' Paper for Experimental Model (Call it just 'Reference') <br/ >  
 
Obo file to be used: Paper obo <br/ >
 
Obo file to be used: Paper obo <br/ >
 
Behavior:Autocomplete obo <br/ >  
 
Behavior:Autocomplete obo <br/ >  
Line 39: Line 44:
 
Multi value. <br/ >
 
Multi value. <br/ >
  
'''Field 4 Name:''' Species <br/ >
+
'''Field 5 Name:''' Species <br/ >
 
Behavior: Auto-complete drop-down with ready values <br/ >
 
Behavior: Auto-complete drop-down with ready values <br/ >
 
Similar to: Project field in the GO OA <br/ >
 
Similar to: Project field in the GO OA <br/ >
Line 45: Line 50:
  
 
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) ? <br/ >
 
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) ? <br/ >
A: Yes, I just spoke to Daneila and adding the value 'Homo sapiens' is fine with her. <br/ >
+
A: Yes, I just spoke to Daniela and adding the value 'Homo sapiens' is fine with her. <br/ >
  
  
'''Field 5 Name''': xref Database <br/ >
+
'''Field 6 Name''': xref Database <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
  
Line 56: Line 61:
  
  
 
+
'''Field 7 Name:''' Disease_relevance <br/ >
'''Field 6 Name:''' Disease_relevance <br/ >
 
 
Behavior: Big Text box (big text-box, keeps expanding) <br/ >
 
Behavior: Big Text box (big text-box, keeps expanding) <br/ >
 
Similar To: 'Description Text' field in the Concise OA. <br/ >  
 
Similar To: 'Description Text' field in the Concise OA. <br/ >  
Line 70: Line 74:
  
 
Q: If so, let me know how to transfer the data. <br/ >
 
Q: If so, let me know how to transfer the data. <br/ >
A:   
+
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: <br/ >
 +
WBGene-->WBGene
 +
Curator-->Curator    
 +
 
 +
 
 +
 
  
'''Field 7 Name:''' Paper for Disease Relevance (Call it just Paper) <br/ >
+
'''Field 8 Name:''' Paper for Disease Relevance (Call it just Reference) <br/ >
 
Behavior: Autocomplete obo <br/ >  
 
Behavior: Autocomplete obo <br/ >  
 
Obo file to be used: WBPaper obo <br/ >
 
Obo file to be used: WBPaper obo <br/ >
Line 82: Line 91:
 
A: Multivalue <br/ >
 
A: Multivalue <br/ >
  
'''Field 8 Name:''' Database <br/ >
+
'''Field 9 Name:''' Database <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
  

Revision as of 21:31, 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?
A: Single value.

Field 2 Name: Curator Behavior of field: Auto-complete drop-down with ready values Similar to: Curator field in GO OA


Field 3 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: Multiple value, as I may need to attach more than one DO term to a gene.

Field 4 Name: Paper for Experimental Model (Call it just 'Reference')
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 5 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) ?
A: Yes, I just spoke to Daniela and adding the value 'Homo sapiens' is fine with her.


Field 6 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.
A: Yes, they will dump as separate lines in the .ace ouput, so then, I will pipe-separate them.


Field 7 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 (?)
A: No, we move this field from the Concise description OA, where its called 'Human disease relevance'.

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:
WBGene-->WBGene Curator-->Curator



Field 8 Name: Paper for Disease Relevance (Call it just Reference)
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 9 Name: 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.


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


I also wanted a GO OA style data table for some of the fields and not for the big Disease_relevance description (which is a big Text box) which we will be moving from the concise description OA.  Wasn't sure if you could have a data table for some fields and not others.

Do you mean that you want this field to exist in the editor but not show below in the data table ?   If so, you can reorder the columns in the data table so it's always right-most, or you can click the label of the field in the editor to grey it out, which hides the column in the data table.  Try it out on any OA, and let me know if that's what you wanted.

Yes, thats fine. I forgot you don't have to see it if you don't want to.