Difference between revisions of "OA and scripts for disease data"
| Line 35: | Line 35: | ||
A: Multiple value, as I may need to attach more than one DO term to a gene. <br/ > | A: Multiple value, as I may need to attach more than one DO term to a gene. <br/ > | ||
| − | '''Field 5 Name:''' | + | '''Field 5 Name:''' Reference for Exp Model <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 64: | Line 64: | ||
| − | '''Field 8 Name:''' | + | '''Field 8 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 71: | Line 71: | ||
Q: So we remove it from the GO OA (?) <br/ > | Q: So we remove it from the GO OA (?) <br/ > | ||
| − | A: No, we move this field from the Concise description OA, where its called 'Human disease relevance'. <br/ > | + | A: No, we move this field from the Concise description OA, where its called 'Human disease relevance' and then remove it (Human Disease Relevance) from the concise OA. <br/ > |
| − | + | ||
Q:Do we start this OA by populating it from existing data in the GO OA ? <br/ > | Q:Do we start this OA by populating it from existing data in the GO OA ? <br/ > | ||
| Line 82: | Line 82: | ||
Curator-->Curator <br/ > | Curator-->Curator <br/ > | ||
Curator History-->Curator History <br/ > | Curator History-->Curator History <br/ > | ||
| − | Description | + | Description Text (Human Disease Relevance)-->Disease Relevance <br/ > |
Reference-->Reference under Disease Relevance <br/ > | Reference-->Reference under Disease Relevance <br/ > | ||
Accession Evidence-->OMIM Database <br/ > | Accession Evidence-->OMIM Database <br/ > | ||
Last Updated-->Last updated | Last Updated-->Last updated | ||
| − | PGID-->PGID | + | PGID-->PGID |
| − | '''Field 9 Name:''' | + | '''Field 9 Name:''' Reference for Disease Rel <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 107: | Line 107: | ||
Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD <br/ > | Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD <br/ > | ||
| − | '''Field 12 Name:''' pgid <br/ > | + | '''Field 12 Name:''' Comment <br/ > |
| + | Behavior: Free text <br/ > | ||
| + | |||
| + | '''Field 13 Name:''' pgid <br/ > | ||
| + | |||
| Line 115: | Line 119: | ||
| − | I also wanted a GO OA style data table for some of the fields and not for the big Disease_relevance description | + | 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) <br/ > |
| − | (which is a big Text box) | ||
| − | |||
| − | Do you mean that you want this field to exist in the editor but not show below in the data table ? | + | Do you mean that you want this field to exist in the editor but not show below in the data table ? <br/ > |
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. <br/ > | 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. <br/ > | ||
Yes, thats fine. I forgot you don't have to see it if you don't want to. | Yes, thats fine. I forgot you don't have to see it if you don't want to. | ||
Revision as of 19:17, 12 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: 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: 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 5 Name: Reference for Exp Model
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: 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: 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: 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' and then remove it (Human Disease Relevance) from the concise 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:
WBGene-->WBGene
Curator-->Curator
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: Reference 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: 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: Last Updated
Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD
Field 12 Name: Comment
Behavior: Free text
Field 13 Name: pgid
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)
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.
