Old pipeline for disease data
Contents
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):
Behavior of field: Autocomplete obo
Source: WBGene obo
Similar to: WBGene in the GO OA or concise descrips OA
As one starts typing locus name, eg, lin-10 or cosmid name, eg., C09H6 script autocompletes and fills in WBGene ID.
Field 2 Curator (dis_curator):
Behavior of field: Auto-complete drop-down with ready values
Similar to: Curator field in GO OA
Field 3 Curator History (dis_curhistory):
Behavior of field: However it is in the concise OA; this is not something that can be changed manually.
Similar to: consise OA
Field 4 Experimental model for (dis_humandoid):
Behavior:Autocomplete obo
Obo file to be used: DO_term obo
Source: https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo
Similar to: GO term field in the GO OA.
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.
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?
A: Everyday at 8pm, if it has the proper .obo format it should be easy to
add to the cronjob that picks them up.
/home/postgres/work/pgpopulation/obo_oa_ontologie/update_obo_oa_ontologies.pl
Field 5 Variation (dis_variation):
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):
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):
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):
Obo file to be used: Paper obo
Behavior:Autocomplete obo
Obo file to be used: WBPaper obo
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
Behavior: Free text, multiple values comma-separated
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.
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
Field 10 Species(dis_species) :
Behavior: Auto-complete drop-down with ready values
Similar to: Project field in the GO OA
Current values: Homo sapiens
Field 11 Last Updated for Exp Model (dis_lastupdateexpmod):
Script autopopulates date when data is a New line, i.e when the "New" button is used.
Field 12 Disease relevance (dis_diseaserelevance)
Behavior: Big Text box (big text-box, keeps expanding)
Similar To: 'Description Text' field in the Concise OA.
It is Human_disease_relevance description (it appears as one of the drop down values) for the'Description Type' field in the 'Concise' OA.
Field 13 Paper for Disease Rel(dis_paperdisrel)
Behavior: Autocomplete obo
Obo file to be used: WBPaper obo
Similar to: The Paper field in the GO OA
Q:So there's two papers fields. Are they both required, or it must have at least one, or nothing is required ?
A: Both are required.
Q:single/multi value ?
A: Multivalue
Field 14 OMIM disease for Disease Rel(dis_dbdisrel) OMIM disease for Disease Rel
Behavior: Free text, multiple values comma-separated
Q:Same as xref Database, but a different field ?
A: Exactly, again I will pipe-separate multiple values.
Field 15 OMIM gene for Disease Rel: Free text, comma separated
Field 16 Last Updated for Disease Rel (dis_lastupdatedisrel):
Behavior: Script fills in current date if new annotation, if manually changing, entered as YYYY-MM-DD
Script autopopulates date when its a new data line.
Field 17 Comment (dis_comment):
Behavior: Free text
Field 18 pgid
Tab 2 of Editor
Field 19 Molecule Type (dis_moleculetype):
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):
Autocomplete drop-down from 'Molecule' class in WormBase
Field 21 Affected Phenotype (dis_phenotypeaffected):
Autocomplete single ontology field, from WormBase Phenotype ontology.
Data constraints
For curators only at the tool level to check if required fields are filled.
These dis_ tables : wbgene curator humandoid paperexpmod species diseaserelevance paperdisrel lastupdatedisrel
WBGene
Curator
Experimental model for
Paper for Exp Mod
Species
Disease relevance
Paper for Disease Rel
Last Updated
To make live:
at : /home/postgres/work/pgpopulation/dis_disease/
create_dis_tables.pl -- create new postgres tables for dis_ disease OA
synchronize OA
transfer_concise_disease.pl -- take 95 entries that have con_desctype = 'Human_disease_relevance' and add them to dis_ tables starting with pgid 1.
Ranjana, manually delete the Human_disease_relevance entries from the concise OA.
remove the Human_disease_relevance option from the OA, resynchronize.
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
Use value: WBGene (take ID only)
Eg: WBGene00003058
Model tag: DB_info Database ?Database ?Database_field Text
Use value(s) in 'xref Database' and in 'OMIM database'
Eg: OMIM:173900 and OMIM:601313, do not take OMIM:173900 again from 'OMIM database' since it is a duplicateof that in 'xref Database'.
.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
Use value in 'Experimental Model for'
Eg:autosomal dominant polycystic kidney (DOID:5937); take ID only
Use value in 'Species' for ?Species
Eg: Homo sapiens
Use value(s) in 'Paper for Disease Rel' for #Evidence
Eg.WBPaper00038373
Repeat .ace line for every paper if multiple papers are present.
.ace:
Experimental_model DOID:5937 "Homo sapiens" Paper_evidence "WBPaper00038373"
Model tag: Disease_relevance ?Text ?Species #Evidence
Use value in 'Disease Relevance' for ?Text
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.
Use value in 'Species' for ?Species
Eg. Homo sapiens
Use value in 'Paper for Disease Rel' for #Evidence
Eg: WBPaper00038373
.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).
So put together, .ace file for lov-1 looks like:
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"
When to dump data
If data is present in Field 4-- (dis_expmodelfor) Experimental model for, dump this field and the related fields:
Field 5 Name:(dis_paperexpmod) Paper for Exp Mod
Field 6 Name:(dis_xrefdb) Database for Exp Mod
Field 7 Name:(dis_species) Species
If data is present in Field 9 Name:(dis_diseaserelevance) Disease relevance, dump this and the related fields:
Field 10 Name:(dis_paperdisrel) Paper for Disease Rel
Field 11 Name:(dis_omimdb) Database for Disease Rel
Field 7 Name:(dis_species) Species
Code annotation
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
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