View source for Old pipeline for disease data

===Ontology Annotator for disease data===

Note: All disease_relevant descriptions have been removed from the concise descriptions OA and moved to the disease OA. 

====Fields====
One gene can be attached to more than one Experimental_Model and one Disease_Relevance (and their related papers, databases and species); they will be grouped together in one instance of the Editor and grouped together in one line in the data-table. This is similar to a gene being attached to more than one GO term. If a gene needs to be attached to a unrelated disease, enter all data on a new line, by hitting 'New' in the OA.

Editor:
'''Tab 1:''' 

'''Field 1 WBGene (dis_wbgene):''' <br/ > 
Behavior of field: Autocomplete obo <br/ >
Source: WBGene obo <br/ >
Similar to: WBGene in the GO OA or concise descrips OA <br/ >
As one starts typing locus name, eg, lin-10 or cosmid name, eg., C09H6 script autocompletes and fills in WBGene ID. <br/ >

'''Field 2 Curator (dis_curator):''' <br/ >
Behavior of field: Auto-complete drop-down with ready values <br/ >
Similar to: Curator field in GO OA <br/ >

'''Field 3 Curator History (dis_curhistory):''' <br/>
Behavior of field: However it is in the concise OA; this is not something that can be changed manually. <br/ >
Similar to: consise OA <br/ >

'''Field 4 Experimental model for (dis_humandoid):''' <br/ >
Behavior:Autocomplete obo <br/ > 
Obo file to be used: DO_term obo <br/ > 
Source: https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo <br/ >
Similar to: GO term field in the GO OA. <br/ >
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. <br/ >

This is a multi value ontology field, but in general use only one disease/row signifying one experiment.

Q:Updating: How do we update this obo file, how frequently do other obo files get updated? <br/ >
A: Everyday at 8pm, if it has the proper .obo format it should be easy to
add to the cronjob that picks them up. <br/ >
/home/postgres/work/pgpopulation/obo_oa_ontologie/update_obo_oa_ontologies.pl <br/ >

'''Field 5 Variation (dis_variation)''': <br/>
Autocomplete dropdown, enter only one variation per row/experiment, right now no way to represent a double mutant, i.e no object exists. DO not enter a transgene as well.

'''Field 6 Disease Phenotype (dis_phenotypedisease):''' <br/>
Multi-ontology field, several disease phenotypes can be entered for a single variation OR a single transgene, but not both.

'''Field 7 Transgene (dis_transgene):''' <br/>
Autocomplete drop-down, allows only one, if transgene is entered do not enter a variation and vice versa.

'''Field 8 Paper for Exp Mod (dis_paperexpmod):''' <br/ > 
Obo file to be used: Paper obo <br/ >
Behavior:Autocomplete obo <br/ > 
Obo file to be used: WBPaper obo <br/ >
Similar to: The Paper field in the GO OA 
this is multivalue

'''Field 9 OMIM disease for Exp Mod(dis_dbexpmod):''' Database for Exp Mod <br/ >
Behavior: Free text, multiple values comma-separated <br/ >
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. <br/ >
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 <br/ >

'''Field 10 Species(dis_species)''' : <br/ >
Behavior: Auto-complete drop-down with ready values <br/ >
Similar to: Project field in the GO OA <br/ >
Current values: Homo sapiens <br/ >

'''Field 11 Last Updated for Exp Model (dis_lastupdateexpmod):''' <br/ >
Script autopopulates date when data is a New line, i.e when the "New" button is used.  <br />

'''Field 12 Disease relevance (dis_diseaserelevance)''' <br/ >
Behavior: Big Text box (big text-box, keeps expanding) <br/ >
Similar To: 'Description Text' field in the Concise OA. <br/ > 
It is Human_disease_relevance description (it appears as one of the drop down values) for the'Description Type' field in the 'Concise' OA. <br/ >

'''Field 13 Paper for Disease Rel(dis_paperdisrel)''' <br/ >
Behavior: Autocomplete obo <br/ > 
Obo file to be used: WBPaper obo <br/ >
Similar to: The Paper field in the GO OA <br/ >

Q:So there's two papers fields.  Are they both required, or it must have at least one, or nothing is required ? <br/ >
A: Both are required. <br/ >
Q:single/multi value ? <br/ >
A: Multivalue <br/ >

'''Field 14 OMIM disease for Disease Rel(dis_dbdisrel) OMIM disease for Disease Rel <br/ >'''
Behavior: Free text, multiple values comma-separated <br/ >

Q:Same as xref Database, but a different field ? <br/ >
A: Exactly, again I will pipe-separate multiple values. <br/ >

'''Field 15 OMIM gene for Disease Rel:''' 
Free text, comma separated

'''Field 16 Last Updated for Disease Rel (dis_lastupdatedisrel):''' <br/ >
Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD <br/ >
Script autopopulates date when its a new data line. <br />

'''Field 17 Comment (dis_comment):''' <br/ >
Behavior: Free text <br/ >

'''Field 18 pgid''' <br/ >

'''Tab 2 of Editor'''<br/ >

'''Field 19 Molecule Type (dis_moleculetype):'''<br/ >
Autocomplete with fixed values--Therapeutic_molecule, Toxic_molecule, Exacerbating_molecule 
Choose only one 'type' per row/per pgid/per disease/per variation/per transgene/per phenotype

'''Field 20 Molecule (dis_molecule):'''<br/ >
Autocomplete drop-down from 'Molecule' class in WormBase

'''Field 21 Affected Phenotype (dis_phenotypeaffected):'''<br/ >
Autocomplete single ontology field, from WormBase Phenotype ontology.

====Data constraints====
For curators only at the tool level to check if required fields are filled. <br/ >
These dis_ tables : wbgene curator humandoid paperexpmod species diseaserelevance paperdisrel lastupdatedisrel
WBGene <br/ >
Curator <br/ >
Experimental model for <br/ >
Paper for Exp Mod <br/ >
Species <br/ >
Disease relevance <br/ >
Paper for Disease Rel <br/ >
Last Updated <br/ >

'''To make live:''' <br/ >
at : /home/postgres/work/pgpopulation/dis_disease/ <br/ >
create_dis_tables.pl -- create new postgres tables for dis_ disease OA <br/ >
synchronize OA <br/ >
transfer_concise_disease.pl -- take 95 entries that have con_desctype = 'Human_disease_relevance' and add them to dis_ tables starting with pgid 1. <br/ >
Ranjana, manually delete the Human_disease_relevance entries from the concise OA. <br/ >
remove the Human_disease_relevance option from the OA, resynchronize. <br/ >

===Dumper specifications===

Dumper module in sandbox at /home/postgres/work/citace_upload/dis_disease/get_dis_disease_ace.pm
Copy /home/postgres/work/citace_upload/dis_disease/use_package.pl to a directory you own and run it there.

===Mapping between OA fields and acedb tags===
Model:

 ?Gene
 DB_info  Database ?Database ?Database_field Text
 Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species   #Evidence	            
              Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence
              Disease_relevance  ?Text ?Species #Evidence

We do not fill in Potential_model tag, Sanger does.

'''The example is lov-1 in the disease OA in the sandbox:'''

'''Model tag: ?Gene''' <br />
Use value: WBGene (take ID only) <br />
Eg: WBGene00003058 <br />

Model tag: DB_info  Database ?Database ?Database_field Text <br />
Use value(s) in 'xref Database' and in 'OMIM database' <br />
Eg: OMIM:173900 and OMIM:601313, do not take OMIM:173900 again from 'OMIM database' since it is a duplicateof that in 'xref Database'. <br />

 .ace:
 Database	 "OMIM"	   "disease"	 "173900"
 Repeat line for each value if there are multiple values

'''Model tag: Experimental_model ?DO_term XREF Gene_by_biology ?Species   #Evidence'''<br />
Use value in 'Experimental Model for' <br />
Eg:autosomal dominant polycystic kidney (DOID:5937); take ID only <br />
Use value in 'Species' for ?Species <br />
Eg: Homo sapiens <br />
Use value(s) in 'Paper for Disease Rel' for #Evidence <br />
Eg.WBPaper00038373 <br />
Repeat .ace line for every paper if multiple papers are present. <br />

.ace: <br />
 Experimental_model  DOID:5937  "Homo sapiens"	Paper_evidence	"WBPaper00038373"	

'''Model tag: Disease_relevance  ?Text ?Species #Evidence''' <br />
Use value in 'Disease Relevance' for ?Text <br />
Eg:lov-1 and pkd-2 encode the orthologs of human Polycystin-1 and Polycystin-2, which are mutated in autosomal dominant polycystic kidney disease; the polycystins regulate signaling involved in normal renal tubular structure and function; studies in the worm C. elegans have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; in elegans lov-1 and pkd-2 are expressed in male ciliary neurons, are required for normal male mating behavior, do not seem to be required for ciliogenesis, and each polycystin may actually have a potential inhibitory function on the other for ciliary function; lov-1 and pkd-1 interact with a single-pass transmembrane protein, CWP-5, though the significance of this interaction for polycystic kidney disease is unknown. <br />

Use value in 'Species' for ?Species <br />
Eg. Homo sapiens

Use value in 'Paper for Disease Rel' for #Evidence <br />
Eg: WBPaper00038373

<pre style="white-space: pre-wrap; 
white-space: -moz-pre-wrap;
white-space: -pre-wrap;
white-space: -o-pre-wrap; 
word-wrap: break-word">
.ace:
Disease_relevance "lov-1 and pkd-2 encode the orthologs of human Polycystin-1 and    Polycystin-2, which are mutated in autosomal dominant polycystic kidney disease; the polycystins regulate signaling involved in normal renal tubular structure and function; studies in the worm C. elegans have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; in elegans lov-1 and pkd-2 are expressed in male ciliary neurons, are required for normal male mating behavior, do not seem to be required for ciliogenesis, and each polycystin may actually have a potential inhibitory function on the other for ciliary function; lov-1 and pkd-1 interact with a single-pass transmembrane protein, CWP-5, though the significance of this interaction for polycystic kidney disease is unknown."	"Homo sapiens"	Paper_evidence	"WBPaper00038373"

(Repeat this line for every paper, if multiple papers are present).
</pre>

'''So put together, .ace file for lov-1 looks like:'''
<pre style="white-space: pre-wrap; 
white-space: -moz-pre-wrap;
white-space: -pre-wrap;
white-space: -o-pre-wrap; 
word-wrap: break-word">
Gene : "WBGene00003058"
Database	"OMIM"	"disease"	"173900"
Database	"OMIM"	"disease"	"601313"
Experimental_model DOID:5937 "Homo sapiens"	Paper_evidence	"WBPaper00038373"	
Disease_relevance	"lov-1 and pkd-2 encode the orthologs of human Polycystin-1 and Polycystin-2, which are mutated in autosomal dominant polycystic kidney disease; the polycystins regulate signaling involved in normal renal tubular structure and function; studies in the worm C. elegans have contributed extensively to the finding that cystic kidney diseases can be considered ciliopathies; in elegans lov-1 and pkd-2 are expressed in male ciliary neurons, are required for normal male mating behavior, do not seem to be required for ciliogenesis, and each polycystin may actually have a potential inhibitory function on the other for ciliary function; lov-1 and pkd-1 interact with a single-pass transmembrane protein, CWP-5, though the significance of this interaction for polycystic kidney disease is unknown."	"Homo sapiens"	Paper_evidence	"WBPaper00038373"
</pre>

====When to dump data====

If data is present in Field 4-- (dis_expmodelfor) Experimental model for, dump this field and the related fields: <br />
Field 5 Name:(dis_paperexpmod) Paper for Exp Mod <br />
Field 6 Name:(dis_xrefdb) Database for Exp Mod <br />
Field 7 Name:(dis_species) Species <br />

If data is present in Field 9 Name:(dis_diseaserelevance) Disease relevance, dump this and the related fields: <br />
Field 10 Name:(dis_paperdisrel) Paper for Disease Rel <br />
Field 11 Name:(dis_omimdb) Database for Disease Rel <br />
Field 7 Name:(dis_species) Species <br />

===Code annotation===
[[Annotation of Disease scripts]]

===Counting script specifications===
Counting script counts numbers in Postgres at any given instance and not from the .ace file.

Script at : /home/acedb/ranjana/human_disease/count_disease.pl 

1. No. of genes (dis_wbgene): Counts all genes including duplicates, lists PGIDs of duplicate genes

2. No. of unique genes : Counts all genes, only once

3. No. of Experimental Models or DO_terms (dis_humandoid): counts all DO_terms

4. No. of unique Experimental models or DO_terms: does not count repeated DO_terms

5. No. of papers for Experimental models or DO_terms (dis_paperexpmod): counts all papers

6. No. of papers for Disease Relevance (dis_paperdisrel)

7. No. of unique papers in all of disease curation: no. of papers in dis_paperexpmod + no. of papers in dis_paperdisrel, counts a paper only once in both categories, no duplicates

8. No. of disease relevance descriptions (dis_diseaserelevance)

9. No. of OMIM genes connected to (WB)genes: from field 12 in OA-'OMIM gene for Disease Rel' entries look like 'OMIM:607485' or just '607485'; entries are comma separated  (What is the Postgres table name? -- dis_genedisrel)

10. No. of OMIM diseases connected to WB genes: from OA Field 'OMIM disease for Exp Mod (dis_dbexpmod) plus (dis_dbdisrel) OA field-OMIM disease for Disease Rel, counts a disease only once, if it appears in both categories; entries look like 'OMIM:607485' or just '607485'; entries are comma separated


Back To [[OA and scripts for disease data]]