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

New fields added, July 2016, to expand the disease term Oa, in order to capture transgene, variation, disease phenotype, molecule and type and affected phenotype.

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	Variation	Autocomplete drop-down	not required	Variation	To be modelled	dit_variation
5	Disease Phenotype	Autocomplete dropdown (multiontology)	required	Disease Phenotype	To be modelled	dit_phenotypedisease
6	Transgene	Autocomplete dropdown (single value only)	required	Transgene	To be modelled	dit_transgene
7	Species	Autocomplete dropdown	required	Homo sapien	?Species	dit_species
8	Worm Model Description	Big text box	required	The C. elegans model for..	Worm_disease_model	dit_wormmodeldesc
9	Paper	Autocomplete obo, multivalue	required	WBPaper00038373 WBPaper00040341	Paper_evidence	dit_paper
10	Date	Autocompleted for new annotation editable for old	required	2014-02-27	Date_last_updated	dit_lastupdate
11	Comment	Free text	optional	Waiting for DO_term..	n/a	dit_comment
12	PGID	Script populates	n/a	48	n/a
13	Molecule Type	Fixed values, three	required	therapeutic_molecule	To be modelled	dit_moleculetype
14	Molecule	Autocomplete, Drop-down, single value	Not required	Reserpine	To be modelled	dit_molecule
15	Affected Phenotype	Auto-complete ontology, single value	protein aggregation variant	To be modelled	dit_phenotypeaffected

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

Back To OA and scripts for disease data