Difference between revisions of "OA for disease term"

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|4 || Species || Autocomplete dropdown || '''required''' || Homo sapien || ?Species || dit_species
 
|4 || Species || Autocomplete dropdown || '''required''' || Homo sapien || ?Species || dit_species
 
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|5 || Worm Model Description||Big text box||'''required'''||The C. elegans model for..|| Worm_model_description||
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|5 || Worm Model Description||Big text box||'''required'''||The C. elegans model for..|| Worm_model_description
|dit_wormmodeldesc
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||dit_wormmodeldesc
 
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|6 || Paper || Autocomplete obo, multivalue || '''required'''|| WBPaper00038373<br/>WBPaper00040341 ||Paper_evidence||dit_paper  
 
|6 || Paper || Autocomplete obo, multivalue || '''required'''|| WBPaper00038373<br/>WBPaper00040341 ||Paper_evidence||dit_paper  
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'''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====
 
====Location of disease data====

Revision as of 18:47, 28 February 2014

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_model_description 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

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