OA for disease term

In cases where there is no elegans gene to attach disease data (eg., Huntington's disease), data will be attached to the DO-term.

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

Field descriptions for 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 term data

/home/acedb/ranjana/human_disease/diseaseterm

run use_package.pl to dump diseaseterm data from the Disease Term OA.

For Juancarlos (done)

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_disease_model        "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_disease_model       "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_disease_model	   "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_disease_model	   "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_disease_model     "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