Model changes to capture and consolidate human disease data
From WormBaseWiki
Contents
- 1 Gene class proposal (April 2020)
- 2 Variation class proposal (April 2020)
- 3 Strain class proposal (April 2020)
- 4 Genotype class proposal (April 2020)
- 5 Transgene class proposal (April 2020)
- 6 DO_term class proposal (April 2020)
- 7 Disease_model_annotation class proposal (April 2020)
- 8 Disease Ontology .obo to AceDB tag mapping
- 9 Adding Disease Ontology as a ?Database object - DONE
- 10 Linking back to the Disease Ontology
- 11 Disease Ontology Browser REST API
- 12 Disease Data dumping for citace uploads
- 13 New class: Disease_model_annotation and related changes, Feb 2017
Gene class proposal (April 2020)
- Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Disease_relevant_gene
- Add 3 new tags
?Gene
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
Modifies_disease ?DO_term XREF Disease_modifier_gene //New tag
Models_disease_in_annotation ?Disease_model_annotation XREF Disease_relevant_gene//New tag
Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_gene//New tag
Variation class proposal (April 2020)
- Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Variation
- Add 3 new tags
?Variation
Disease_info Models_disease ?DO_term XREF Disease_model_variation
Modifies_disease ?DO_term XREF Disease_modifier_variation //New tag
Models_disease_in_annotation ?Disease_model_annotation XREF Variation //New tag
Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_variation//New tag
Strain class proposal (April 2020)
- Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Strain
- Add 3 new tags
?Strain
Disease_info Models_disease ?DO_term XREF Disease_model_strain
Modifies_disease ?DO_term XREF Disease_modifier_strain //New tag
Models_disease_in_annotation ?Disease_model_annotation XREF Strain //New tag
Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_strain //New tag
Genotype class proposal (April 2020)
?Genotype
Disease_info Models_disease ?DO_term XREF Disease_model_genotype
Modifies_disease ?DO_term XREF Disease_modifier_genotype
Models_disease_in_annotation ?Disease_model_annotation XREF Genotype
Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_genotype
Transgene class proposal (April 2020)
- Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Transgene
- Add 3 new tags
?Transgene
Disease_info Models_disease ?DO_term XREF Disease_model_transgene
Modifies_disease ?DO_term XREF Disease_modifier_transgene //New tag
Models_disease_in_annotation ?Disease_model_annotation XREF Transgene //New tag
Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_transgene //New tag
DO_term class proposal (April 2020)
- 4 new tags
?DO_term
Attribute_of Gene_by_biology ?Gene XREF Experimental_model
Gene_by_orthology ?Gene XREF Potential_model
Disease_modifier_gene ?Gene XREF Modifies_disease //New tag
Phenotype ?Phenotype XREF DO_term
WBProcess ?WBProcess XREF DO_term
Reference ?Paper XREF DO_term
Disease_model_variation ?Variation XREF Models_disease
Disease_modifier_variation ?Variation XREF Modifies_disease //New tag
Disease_model_strain ?Strain XREF Models_disease
Disease_modifier_strain ?Strain XREF Modifies_disease //New tag
Disease_model_transgene ?Transgene XREF Models_disease
Disease_modifier_transgene ?Transgene XREF Modifies_disease //New tag
Disease_model_genotype ?Genotype XREF Models_disease
Disease_modifier_genotype ?Genotype XREF Modifies_disease
Chemical_inducer ?Molecule XREF Induces_disease
Other_inducer ?Text //New tag
Molecule_modifier ?Molecule XREF Modifies_disease
.ace file example
- Rule for the dumper: for a given DO_term (Disease name in OA) collect below entitities from the disease OA and dump under "DO_term" object.
- Disease relevant gene
- Variation (dis_variation)
- Strain (dis_strain)
- Transgene (dis_transgene)
- Genotype (dis_genotype) //Add for WS278
- Modifier transgene (dis_modtransgene)//Add for WS278
- Modifier variation (dis_modvariation)//Add for WS278
- Modifier strain (dis_modstrain) // Add for WS278
- Modifier gene (dis_modgene) //Add for WS278
- Modifier genotype (dis_modgenotype) //Add for WS278
- Modifier genotype //Add for WS278
- Inducing chemical (dis_inducingchemical)
- Inducing agent (dis_inducingagent )(acedb tag: Other_inducer) //Add for WS278
- Modifier molecule (dis_modmolecule)
DO_term : "DOID:10652" Disease_modifier_strain "WBStrain00005113" //Add Modifier strains from OA Disease_modifier_variation "WBVar02146626" //Add Modifier variations from OA Disease_modifier_gene "WBGene00000097" //Add Modifier genes from OA Disease_model_genotype "WBGenotype00000001" //Add genotypes from OA Disease_modifier_genotype "<WBGenotypeXXXXXXXX>" //Add modifier genotype from OA
Disease_model_annotation class proposal (April 2020)
- Remove the XREF to Disease_model_annotation for Strain, Variation, Transgene, and Disease_relevant_gene tags
- Add the XREF to Models_disease_in_annotation for Strain, Varation, Transgene, and Disease_relevant_gene tags
- Add XREFS to all Modifier lines
?Disease_model_annotation
Modeled_by Strain UNIQUE ?Strain XREF Models_disease_in_annotation ?Text //Changed XREF
Variation UNIQUE ?Variation XREF Models_disease_in_annotation ?Text//Changed XREF
Transgene UNIQUE ?Transgene XREF Models_disease_in_annotation ?Text//Changed XREF
Disease_relevant_gene UNIQUE ?Gene XREF Models_disease_in_annotation ?Text //Changed XREF
Evidence_code ECO_term ?ECO_term //new tag
GO_code ?GO_code //old tag, but add "GO_code" in front of ?GO_code
Modifier_info Modifier_transgene ?Transgene XREF Modifies_disease_in_annotation //XREF added
Modifier_variation ?Variation XREF Modifies_disease_in_annotation //XREF added
Modifier_strain ?Strain XREF Modifies_disease_in_annotation //XREF added
Modifier_gene ?Gene XREF Modifies_disease_in_annotation //XREF added
Modifier_molecule ?Molecule XREF Disease_model_modifier
Other_modifier ?Text
Disease Ontology .obo to AceDB tag mapping
Source of files
SourceForge repo of multiple DO files.
http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/HumanDO.obo disease ontology .obo file
Example obo and .ace formats
obo: [Term] id: DOID:0050047 name: Flinders Island spotted fever alt_id: DOID:0050048 def: "A spotted fever that has_material_basis_in Rickettsia honei, which is transmitted_by cayenne ticks (Amblyomma cajennense). The infection has_symptom mild spotted fever, has_symptom eschar and has_symptom adenopathy." [url:http\://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2003.tb07338.x/pdf, url:http\://www.cdc.gov/otherspottedfever/index.html] subset: gram-negative_bacterial_infectious_disease subset: tick-borne_infectious_disease synonym: "FISF" RELATED [] synonym: "Thai tick typhus" EXACT [] is_a: DOID:11104 ! spotted fever .ace: DO_term : "DOID:0050046" Name "Flinders Island spotted fever" Status Valid Alternate_id "DOID:0050048" Definition "A spotted fever that has_material_basis_in Rickettsia honei, which is transmitted_by cayenne ticks (Amblyomma cajennense). The infection has_symptom mild spotted fever, has_symptom eschar and has_symptom adenopathy." Synonymn Related "FISF" Synonymn Exact "Thai tick typhus" Is_a "DOID:11104" Type "Gram_negative_bacterial_infectious_disease" Type "Tick_borne_infectious_disease" Version "2586" obo: [Term] id: DOID:0050119 name: West Nile virus neurological syndrome def: "A West Nile virus infectious disease that has_material_basis_in West Nile virus, which can cause meningitis, encephalitis, acute laccid paralysis, Parkingsonian-like conditions or movement disorder." [URL:http\://www.phac-aspc.gc.ca/wnv-vwn/hmncasedef-eng.php] subset: zoonotic_infectious_disease synonym: "West nile neuroinvasive disease" EXACT [] synonym: "WNND" EXACT [] synonym: "WNNS" EXACT [] is_obsolete: true .ace: DO_term : "DOID:0050119" Name "West Nile virus neurological syndrome" Status Obsolete Definition "A West Nile virus infectious disease that has_material_basis_in West Nile virus, which can cause meningitis, encephalitis, acute laccid paralysis, Parkingsonian-like conditions or movement disorder." Synonymn Exact "West nile neuroinvasive disease" Synonymn Exact "WNND" Synonymn Exact "WNNS" Type "Zoonotic_infectious_disease" Version "2586" obo: [Term] id: DOID:0050156 name: idiopathic pulmonary fibrosis def: "A idiopathic interstitial pneumonia which is a distinctive type of chronic fibrosing interstitial pneumonia with thick scarring in the lung creating a honeycomb appearance. The main symptoms start insidiously as shortness of breath on exertion, cough, and diminished stamina. Other common complaints include weight loss and fatigue. The level of oxygen in the blood decreases, and the skin may take on a bluish tinge (called cyanosis) and the ends of the fingers may become thick or club-shape. In most people, symptoms worsen over a period ranging from about 6 months to several years." [url:http\://www.merck.com/mmhe/sec04/ch050/ch050b.html?qt=idiopathic%20interstitial%20pneumonia&alt=sh, url:http\://www.ncbi.nlm.nih.gov/pubmed/11790668] comment: OMIM mapping confirmed by DO. [SN]. synonym: "cryptogenic fibrosing alveolitis" EXACT [] synonym: "FIBROCYSTIC PULMONARY DYSPLASIA" EXACT [] synonym: "IDIOPATHIC PULMONARY FIBROSIS, FAMILIAL" EXACT [] xref: MSH:D054990 xref: OMIM:178500 is_a: DOID:2797 ! idiopathic interstitial pneumonia .ace: DO_term : "DOID:0050156" Name "idiopathic pulmonary fibrosis" Status Valid Definition "A idiopathic interstitial pneumonia which is a distinctive type of chronic fibrosing interstitial pneumonia with thick scarring in the lung creating a honeycomb appearance. The main symptoms start insidiously as shortness of breath on exertion, cough, and diminished stamina. Other common complaints include weight loss and fatigue. The level of oxygen in the blood decreases, and the skin may take on a bluish tinge (called cyanosis) and the ends of the fingers may become thick or club-shape. In most people, symptoms worsen over a period ranging from about 6 months to several years." Comment "OMIM mapping confirmed by DO." Synonymn Exact "cryptogenic fibrosing alveolitis" Synonymn Exact "FIBROCYSTIC PULMONARY DYSPLASIA" Synonymn Exact "IDIOPATHIC PULMONARY FIBROSIS, FAMILIAL" Is_a "DOID:2797" Database "OMIM" "disease" "178500" Version "2586"
Adding Disease Ontology as a ?Database object - DONE
We should probably add the DO as a Database object:
Disease_ontology Name Disease Ontology Description The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease concepts through collaborative efforts of researchers at Northwestern University, Center for Genetic Medicine and the University of Maryland School of Medicine, Institute for Genome Sciences. URL http://www.disease-ontology.org URL_constructor - is there such a thing for this database?
I'll add this into geneace as this is the primary source of this class. (Paul D.)
Database : "Disease_ontology" Name "Disease Ontology" Description "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease concepts through collaborative efforts of researchers at Northwestern University, Center for Genetic Medicine and the University of Maryland School of Medicine, Institute for Genome Sciences." URL "http:\/\/www.disease-ontology.org"
Linking back to the Disease Ontology
primarily for the DB_info tags, currently it is not possible to link back to http://disease-ontology.org as they employ a java browser within the page to serve tabs of data :(
I was in contact with Cesar Arze about that issue and they provided the following url that might be ok for the short term until they develop the functionality.
http://disease-ontology.org/term/DOID%3A<DOID>
Example for DOID1115
Might be useable for now......ask Todd.
Disease Ontology Browser REST API
- Might be worth mentioning this to Todd as he might be able to code something funky from their API.
A RESTful API service is also offered to users of the Disease Ontology browser website to allow for programmatic access to the metadata found in the database.
Metadata returned in JSON format may currently be requested by use of the following URL:
http://www.disease-ontology.org/api/metadata/<DOID>
Example usage here would be querying for metadata from the term "Disease" (DOID:4):
http://www.disease-ontology.org/api/metadata/DOID:4
which would return the following JSON:
{ definition: ""A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [url:http\://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf]" -xrefs: [ "MSH2010_2010_02_22:D004194" "NCI2009_04D:C2991" "SNOMEDCT_2010_1_31:64572001" "UMLS_CUI:C0012634" ] -children: [ -[ "disease of cellular proliferation" "DOID:14566" ] -[ "medical disorder" "DOID:0060035" ] -[ "disease of anatomical entity" "DOID:7" ] -[ "disease of metabolism" "DOID:0014667" ] -[ "genetic disease" "DOID:630" ] -[ "disease of mental health" "DOID:150" ] -[ "disease by infectious agent" "DOID:0050117" ] -[ "syndrome" "DOID:225" ] ] name: "disease" id: "DOID:4" }
In the future we hope to offer all the services that are available on the Disease Ontology browser website through the REST API as well.
Disease Data dumping for citace uploads
All scripts are under: /home/acedb/ranjana/human_disease
1. parseHuman.pl:
- Downloads the HumanDO.obo from http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/HumanDO.obo and converts it to HumanDO.ace.
- Upload to Spica under Data_for_citace/Data_from_Ranjana/. Change name to HumanDO_WSXXX.ace
2. use_package.pl: Dumps disease data from the disease OA, into disease_<date>.ace Upload to Spica under Data_for_citace/Data_from_Ranjana/. Change name to disease_WSXXX.ace
3. Download the HumanDO.obo file from http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/HumanDO.obo and rename as disease_ontology.WSXXX.obo.
Disease_model_annotation Class, Proposed by Ranjana, Feb, 2017
Changes for WS260
- 'UNIQUE' before DO_term in Disease_name tag, actually changed Disease_name tag to Disease_term tag, suggested by KH.
- Added new tag: Disease_of_Species ?Species (to indicate what species the disease naturally occurs in)
- UNIQUE added before ?Strain, ?Variation, ?Transgene, and ?Gene in the sub-tags for Modeled_by, because I should be able to use multiple genetic entities but only one of each kind. There would be a preference rule for the DAF, for selection of the type of DB Object in this order--Variation, Strain, Gene, Transgene (when all or some of these are present).
- Disease_relevant_gene tag moved to be a sub-tag of 'Modeled_by', as it's a genetic entity similar to Strain, Variation etc.
- Added a new tag: Inferred_gene, to indicate the implicated gene when a disease is modeled by a Strain, Variation, or Transgene; authors may or may not tell us this, in elegans papers they usually do. Also makes the modeling cleaner and clearer for mapping of acedb tags to DAF columns and OA fields!
- Changed Disease_phenotype_comment to Phenotype_comment
- Added new tag: Disease_model_description ?Text (to describe the disease model in a human readable text paragraph (I have this curated data in our local curation database)
Changes to model for WS262
- Add new tag: Modifier_qualifier NOT
- Add new tag under Annotation_made_with: Interacting_gene ?Gene
- Add new tag under Association_type: is_implicated_in (Eventually we will delete the tags causes_or_contributes_to_condition, causes_condition, contributes_to_condition, after all the data is moved to is_implicated_in).
Current Disease_model_annotation acedb model
?Disease_model_annotation Disease_term UNIQUE ?DO_term XREF Disease_model_annotation
Disease_of_species ?Species
Modeled_by Strain UNIQUE ?Strain XREF Disease_model_annotation ?Text //genetic entity that
models the disease
Variation UNIQUE ?Variation XREF Disease_model_annotation ?Text //genetic entity that
models the disease
Transgene UNIQUE ?Transgene XREF Disease_model_annotation ?Text //genetic entity that
models the disease
Disease_relevant_gene UNIQUE ?Gene XREF Disease_model_annotation ?Text //when the gene is the annotation object
Annotation_made_with Interacting_variation ?Variation //Addition for WS261 to match 'Additional genetic components' of AGR data modeling
Interacting_transgene ?Transgene
Interacting_gene ?Interacting_gene //Addition for WS262 to match AGR DWG data model
RNAi_experiment ?RNAi
Inferred_gene ?Gene //to indicate the gene in Variation or Strain, when submitted
Association_type UNIQUE is_model_of // All 5 tags describe the relationship
between the genetic entity and the disease
is_implicated_in //Add for WS262 to match 'Additional genetic components' of AGR data model
causes_or_contributes_to_condition
causes_condition
contributes_to_condition
is_marker_for
Evidence_code ?GO_code // will use ECO later on
Qualifier NOT //Delete for WS262
Qualifier_not //Add for WS262 to represent 'NOT' disease models
Experimental_condition Inducing_chemical ?Molecule XREF Disease_model_inducer //to indicate
the disease-inducing agent
Inducing_agent ?Text //e.g. diet, radiation,etc not in Molecule class
Modifier_info Modifier_transgene ?Transgene //genetic entity that modifies the disease
Modifier_variation ?Variation //(same as above)
Modifier_strain ?Strain //(same as above)
Modifier_gene ?Gene //to indicate the gene in the modifying
Transgene, Variation, Strain.
Modifier_molecule ?Molecule XREF Disease_model_modifier // to indicate
chemical modifiers of the disease
Other_modifier ?Text //to indicate other modifiers of the disease eg.
diet,radiation, surgery etc
Modifier_association_type UNIQUE condition_ameliorated_by //to indicate the association type between modifiers and disease
condition_exacerbated_by
Modifier_qualifier_not //Add for WS262 Better way for representing NOT for Modifier and disease model associations
Genetic_sex UNIQUE hermaphrodite //indicates genetic sex of the disease model
male
female
Disease_phenotype_info Disease_phenotype ?Phenotype //Phenotypes similar to human disease
Ameliorated_phenotype ?Phenotype // Phenotypes ameliorated by modifier
Exacerbated_phenotype ?Phenotype // Phenotypes exacerbated by modifier
Phenotype_comment ?Text // To describe non-WPO phenotypes
Paper_evidence UNIQUE ?Paper// Addition of 'UNIQUE' for WS261
Disease_model_description ?Text
DB_info Database ?Database ?Database_field ?Text //To indicate the OMIM gene/disease
Curator_confirmed ?Person //caused problems in WS260 as tag was 'Curator_confirmed ?Curator'
Date_last_updated UNIQUE DateType
Sample .ace file
Disease_model_annotation : "00000001" Disease_term "DOID:14330" Disease_of_species "Homo sapiens" Strain "CL4176" Association_type is_model_of Evidence_code "IMP" Inducing_chemical "WBMol:00002044" Modifier_gene "WBGene00010882" Modifier_association_type condition_ameliorated_by Genetic_sex hermaphrodite Disease_phenotype "WBPhenotype:0001935" Disease_phenotype "WBPhenotype:0002426" Ameliorated_phenotype "WBPhenotype:0001935" Paper_evidence "WBPaper00031384" Disease_model_description "In an elegans model of Parkinson's disease, where human alpha-synuclein was overexpressed, RNA interference studies showed that the elegans atg-7/ATG7 (ubiquitin-activating E1 enzyme-like protein), significantly protected against age and dose-dependent degeneration in the dopamine neurons of transgenic worms." Database "OMIM" "gene" "608309" Database "OMIM" "disease" "605909" Curator_confirmed "WBPerson324" Date_last_updated "2017-03-13" Disease_model_annotation : "00000002" Disease_term "DOID:10652" Disease_of_species "Homo sapiens" Strain "CL4176" Association_type is_model_of Evidence_code "IMP" Genetic_sex hermaphrodite Modifier_molecule "WBMol:00004468" Modifier_association_type condition_ameliorated_by Ameliorated_phenotype "WBPhenotype:0001935" Paper_evidence "WBPaper00028904" Disease_model_description "A transgenic model of Alzheimer's disease in C. elegans where the expression of human beta amyloid protein (Abeta) in muscle cells causes Abeta aggregation induced paralysis; treatment with Ginkgo biloba extraxt ginkgolide J alleviates Abeta induced paralysis and inhibits Abeta oligomerization." Database "OMIM" "gene" "608309" Database "OMIM" "disease" "605909" Curator_confirmed "WBPerson324" Date_last_updated "2017-03-13"
Current Gene class (as relates to disease)
?Gene 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
Disease_model_annotation ?Disease_model_annotation XREF Disease_relevant_gene//New class to capture the richness of disease data
Changes to DO_term class
?DO_term Disease_model_annotation ?Disease_model_annotation XREF Disease_term //to hold all the details of a
disease model
Attribute_of Disease_model_variation ?Variation XREF Models_disease //To associate Variations to a disease
Disease_model_strain ?Strain XREF Models_disease //To associate Strains to a disease
Disease_model_transgene ?Transgene XREF Models_disease //To associate Transgenes to disease
Chemical_inducer ?Molecule XREF Induces_disease //To associate inducing chemicals
to a disease
Molecule_modifier ?Molecule XREF Modifies_disease //To associate modifying
chemicals to a disease
Current Variation, Strain, Transgene and Molecule classes
?Variation Disease_info Models_disease ?DO_term XREF Disease_model_variation
Disease_model_annotation ?Disease_model_annotation XREF Variation
?Strain Disease_info Models_disease ?DO_term XREF Disease_model_strain
Disease_model_annotation ?Disease_model_annotation XREF Strain
?Transgene Disease_info Models_disease ?DO_term XREF Disease_model_transgene
Disease_model_annotation ?Disease_model_annotation XREF Transgene
?Molecule Disease_info Induces_disease ?DO_term XREF Chemical_inducer
Modifies_disease ?DO_term XREF Molecule_modifier
Disease_model_inducer ?Disease_model_annotation XREF Inducing_chemical
Disease_model_modifier ?Disease_model_annotation XREF Modifier_molecule
Comment to be addressed:
3) Not all tags are XREF both ways...is this intentional?
Please see the XREFs added to the Disease_model_annotation class, in the following tags: Strain, Variation, Transgene and Disease_relevant_gene. Does this now satisfy the XREFing we wanted from both ways--from Disease_model_annotation to the genetic entity (strain, variation, transgene, gene) and from the genetic entities to Disease_model_annotation.
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