OA for disease term
From WormBaseWiki
Revision as of 19:47, 28 February 2014 by Rkishore (talk | contribs) (→Fields for the Disease Term OA)
In cases where there is no elegans gene to attach disease data (eg., Huntington's disease), data will be attached to the DO-term.
Contents
DO term model
?DO_term Name UNIQUE ?Text Status UNIQUE Valid Obsolete Alternate_id ?Text Definition UNIQUE ?Text Worm_disease_model ?Text ?Species #Evidence //added Jan 2014, for WS242 Comment Text Synonymn Broad ?Text Exact ?Text Narrow ?Text Related ?Text Parent Is_a ?DO_term XREF Is Child Is ?DO_term XREF Is_a DB_info Database ?Database ?Database_field Text Type GOLD Gram_negative_bacterial_infectious_disease Gram_positive_bacterial_infectious_disease Sexually_transmitted_infectious_disease Tick_borne_infectious_disease Zoonotic_infectious_disease Attribute_of Gene_by_biology ?Gene XREF Experimental_model Gene_by_orthology ?Gene XREF Potential_model Phenotype ?Phenotype XREF DO_term WBProcess ?WBProcess XREF DO_term Reference ?Paper XREF DO_term Version UNIQUE Text
Fields for the Disease Term OA
Order | Name | Type | Required? | Shows in OA as | acedb tag | Postgres table name |
---|---|---|---|---|---|---|
1 | DO term | Autocomplete obo | required | Huntington's disease (DOID:12858) | ?DO_term | dit_doterm |
2 | Curator | Autocomplete dropdown | required | Ranjana Kishore | Curator_confirmed | dit_curator |
3 | Curator History | script populates | n/a | 56 | n/a | dit_curhistory |
4 | Species | Autocomplete dropdown | required | Homo sapien | ?Species | dit_species |
5 | Worm Model Description | Big text box | required | The C. elegans model for.. | Worm_disease_model | dit_wormmodeldesc |
6 | Paper | Autocomplete obo, multivalue | required | WBPaper00038373 WBPaper00040341 |
Paper_evidence | dit_paper |
7 | Date | Autocompleted for new annotation editable for old |
required | 2014-02-27 | Date_last_updated | dit_lastupdate |
8 | Comment | Free text | optional | Waiting for DO_term.. | n/a | dit_comment |
9 | PGID | Script populates | n/a | 48 | n/a |
Note: Creating a new annotation row by clicking 'new' in the data table, generates the pgid, the curator, and the date last updated.
Location of disease data
/home/acedb/ranjana/human_disease
To make scripts live: To make live on tazendra remind me to :
- create tables with
/home/postgres/work/pgpopulation/dit_diseaseterm/
- sync the OA
- copy the dumper at
/home/postgres/work/citace_upload/dit_diseaseterm/
The use_package.pl is at
/home/postgres/work/citace_upload/dit_diseaseterm/use_package.pl
So you can symlink it to the acedb account wherever you want it, and then run it.
Example .ace file
DO_term : "DOID:12858" Worm_model_description "The human ortholog of arl-6, ADP-ribosylation factor-like 6 (ARL6) also known as BBS3, is mutated in Bardet-Biedl syndrome 3; Bardet-Biedl syndrome phenotypes include retinal degeneration, obesity, renal malformations, polydactyly and learning disabilities; studies in the worm have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; most of the known BBS proteins in human and elegans encode basal body or cilia proteins involved in ciliary structure and function including intraflagellar transport (IFT); studies in elegans indicate that transcription of BBS proteins is regulated by a RFX-transcription factor and that BBS proteins may also regulate GCY-35/GCY-36 cGMP signaling which can affect BBS mutant gene phenotypes." "Homo sapiens" Paper_evidence "WBPaper00038373" Worm_model_description "The human ortholog of arl-6, ADP-ribosylation factor-like 6 (ARL6) also known as BBS3, is mutated in Bardet-Biedl syndrome 3; Bardet-Biedl syndrome phenotypes include retinal degeneration, obesity, renal malformations, polydactyly and learning disabilities; studies in the worm have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; most of the known BBS proteins in human and elegans encode basal body or cilia proteins involved in ciliary structure and function including intraflagellar transport (IFT); studies in elegans indicate that transcription of BBS proteins is regulated by a RFX-transcription factor and that BBS proteins may also regulate GCY-35/GCY-36 cGMP signaling which can affect BBS mutant gene phenotypes." "Homo sapiens" Paper_evidence "WBPaper00040341" Worm_model_description "The human ortholog of arl-6, ADP-ribosylation factor-like 6 (ARL6) also known as BBS3, is mutated in Bardet-Biedl syndrome 3; Bardet-Biedl syndrome phenotypes include retinal degeneration, obesity, renal malformations, polydactyly and learning disabilities; studies in the worm have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; most of the known BBS proteins in human and elegans encode basal body or cilia proteins involved in ciliary structure and function including intraflagellar transport (IFT); studies in elegans indicate that transcription of BBS proteins is regulated by a RFX-transcription factor and that BBS proteins may also regulate GCY-35/GCY-36 cGMP signaling which can affect BBS mutant gene phenotypes." "Homo sapiens" Curator_confirmed "WBPerson324" Worm_model_description "The human ortholog of arl-6, ADP-ribosylation factor-like 6 (ARL6) also known as BBS3, is mutated in Bardet-Biedl syndrome 3; Bardet-Biedl syndrome phenotypes include retinal degeneration, obesity, renal malformations, polydactyly and learning disabilities; studies in the worm have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; most of the known BBS proteins in human and elegans encode basal body or cilia proteins involved in ciliary structure and function including intraflagellar transport (IFT); studies in elegans indicate that transcription of BBS proteins is regulated by a RFX-transcription factor and that BBS proteins may also regulate GCY-35/GCY-36 cGMP signaling which can affect BBS mutant gene phenotypes." "Homo sapiens" Date_last_updated "2014-02-27" Mapping of .ace to fields of OA: DO_term : "DOID:12858" comes from 'DO term' field Worm_model_description "The human ortholog of arl-6,.. comes from 'Worm Model description' field "Homo sapiens" comes from 'Species' field Paper_evidence "WBPaper00038373" comes from 'Paper' field Paper_evidence "WBPaper00040341" comes from 'Paper' field (Repeated for however many papers there are in 'Paper' field). Curator_confirmed "WBPerson324" comes from 'Curator' field Date_last_updated "2014-02-27" comes from 'Date' field