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

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Line 24: Line 24:
 
/home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl <br/ >
 
/home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl <br/ >
  
Q:Single value / multivalue ?
+
Q: Single value / multivalue ?
A:  
+
A: Multiple value, as I may need to attach more than one DO term to a gene.
  
'''Field 3 Name:''' Paper for Experimental Model <br/ >  
+
'''Field 3 Name:''' Paper for Experimental Model (Call it just Paper) <br/ >  
Obo file to be used: DO_term obo <br/ >
+
Obo file to be used: Paper 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  
 
Q: You mean the papers in the paper editor ?
 
Q: You mean the papers in the paper editor ?
 +
The Paper obo, I guess they all come from the Paper Editor.
 +
 
Q:Single/multi ?
 
Q:Single/multi ?
 
+
Multi value.
  
 
'''Field 4 Name:''' Species <br/ >
 
'''Field 4 Name:''' Species <br/ >
Line 43: Line 45:
 
Q:Do you want to use the same list as everyone
 
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) ?
 
else, and add new values to it (if they're okay with those values) ?
 +
A: Yes, I just spoke to Daneila and adding the value 'Homo sapiens' is fine with her.
 +
  
 
'''Field 5 Name''': xref Database <br/ >
 
'''Field 5 Name''': xref Database <br/ >
 
Behavior: Free text, multiple values comma-separated
 
Behavior: Free text, multiple values comma-separated
 +
 
Q: Will they dump in separate lines in the output ?  Usually those are
 
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
 
pipe-separated.  If they'll dump literally as pasted in, then commas
 
are good.
 
are good.
 +
A: Yes, they will dump as separate lines in the .ace ouput, so then, I will pipe-separate them.
 +
 +
  
 
'''Field 6 Name:''' Disease_relevance <br/ >
 
'''Field 6 Name:''' Disease_relevance <br/ >
Line 55: Line 63:
 
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/ >
 +
 
Q: So we remove it from the GO 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 ?
+
A: No, we move this field from the Concise description OA, where its called 'Human disease relevance'.
If so, let me know how to transfer the data.
+
 
 +
Q:Do we start this OA by populating it from existing data in the GO OA ?
 +
A:We can.
 +
 
 +
Q: If so, let me know how to transfer the data.
 +
A: 
  
'''Field 7 Name:''' Paper for Disease Relevance <br/ >
+
'''Field 7 Name:''' Paper for Disease Relevance (Call it just Paper) <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 <br/ >
 
Similar to: The Paper field in the GO OA <br/ >
  
Q:So there's two papers fields.  Are they both required, or it must have
+
Q:So there's two papers fields.  Are they both required, or it must have at least one, or nothing is required ? <br/ >
at least one, or nothing is required ?
+
A: Both are required. <br/ >
single/multi value ?
+
Q:single/multi value ? <br/ >
 +
A: Multivalue <br/ >
  
 
'''Field 8 Name:''' Database <br/ >
 
'''Field 8 Name:''' Database <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
 
Behavior: Free text, multiple values comma-separated <br/ >
Same as xref Database, but a different field ?
 
  
It would probably be better if the labels were shorter (particularly 3
+
Q:Same as xref Database, but a different field ? <br/ >
and 7), the labels in the editor have to match the column labels in
+
A: Exactly, again I will pipe-separate multiple values. <br/ >
data table.
+
 
 +
 
 +
It would probably be better if the labels were shorter (particularly 3and 7), <br/ >
 +
The labels in the editor have to match the column labels in data table. <br/ >
 +
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.
 +
 
 +
 
 +
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.
  
Fields 1-5 will have a data-table associated with them, similar to the GO OA. <br/ >
+
Do you mean that you want this field to exist in the editor but not
Data Table Columns: <br/ >
+
show below in the data table ?  If so, you can reorder the columns in
WBGene <br/ >
+
the data table so it's always right-most, or you can click the label of
Experimental Model For <br/ >
+
the field in the editor to grey it out, which hides the column in the
Paper <br/ >
+
data table.  Try it out on any OA, and let me know if that's what you
Species <br/ >
+
wanted.
xref Database <br/ >
+
Yes, thats fine. I forgot you don't have to see it if you don't want to.

Revision as of 21:02, 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: 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 3 Name: Paper for Experimental Model (Call it just Paper)
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 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) ? A: Yes, I just spoke to Daneila and adding the value 'Homo sapiens' is fine with her.


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


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 (?) 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:We can.

Q: If so, let me know how to transfer the data. A:

Field 7 Name: Paper for Disease Relevance (Call it just Paper)
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 8 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.


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.