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

From WormBaseWiki
Jump to navigationJump to search
Line 3: Line 3:
 
Editor:
 
Editor:
  
'''Field 1 Name:''' WBGene<br/ >  
+
'''Field 1 Name:''' WBGene <br/ >  
Behavior of field: Autocomplete obo<br/ >
+
Behavior of field: Autocomplete obo <br/ >
Source: WBGene obo<br/ >
+
Source: WBGene obo <br/ >
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/ >
  
'''Field 2 Name:''' Experimental model for<br/ >
+
'''Field 2 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/ >  
Source: https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo<br/ >
+
Source: https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo <br/ >
Similar to: GO term field in the GO OA.<br/ >
+
Similar to: GO term field 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/ >
+
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/ >
  
'''Field 3 Name:''' Paper for Experimental Model<br/ >  
+
'''Field 3 Name:''' Paper for Experimental Model <br/ >  
Obo file to be used: DO_term obo<br/ >
+
Obo file to be used: DO_term obo <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/ >
 
Similar to: The Paper field in the GO OA  
 
Similar to: The Paper field in the GO OA  
  
'''Field 4 Name:''' Species<br/ >
+
'''Field 4 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/ >
Current values: Homo sapiens<br/ >
+
Current values: Homo sapiens <br/ >
  
Field 5 Name: xref for DO term
+
Field 5 Name: xref Database
 +
Behavior: Free text, multiple values comma-separated
  
'''Field 6 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/ >  
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.<br/ >
+
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. <br/ >
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.<br/ >
+
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. <br/ >
  
'''Field 7 Name:''' Database<br/ >
+
'''Field 7 Name:''' Database <br/ >
Behavior: Free text, multiple values comma-separated<br/ >
+
Behavior: Free text, multiple values comma-separated <br/ >
  
  
Data Table Columns:
+
Data Table Columns: <br/ >
WBGene
+
WBGene <br/ >
Experimental Model For
+
Experimental Model For <br/ >
Paper
+
Paper <br/ >
Species
+
Species <br/ >
Database
+
Database <br/ >

Revision as of 19:51, 7 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.

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?

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

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: Database
Behavior: Free text, multiple values comma-separated


Data Table Columns:
WBGene
Experimental Model For
Paper
Species
Database