Difference between revisions of "Model changes to capture and consolidate human disease data"
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#Curator | #Curator | ||
#Curator history | #Curator history | ||
− | # | + | #New field: Model_type: Experimental, Predicted, NOT_model (could be Experimental by default) |
#Variation | #Variation | ||
#Change required: Transgene *change to multivalue | #Change required: Transgene *change to multivalue |
Revision as of 20:45, 22 September 2016
Contents
- 1 Gene-disease model discussion
- 2 Gene-disease model
- 3 Proposal for expansion of the Gene-Disease model
- 4 DO_term model
- 5 Proposal for expansion of the DO_term model
- 6 Changes to expand the Disease Term OA
- 7 Older versions
- 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 Model changes to add reagents to disease
- 14 Model changes to associate molecule to disease
Gene-disease model discussion
Paul D's suggestions/corrections for the 'Disease_info' tag under ?Gene::
- Add ?Species tag instead of 'Experimental_model_for_human' type tags, to indicate species information.
Suggestions/Corrections for the ?DO_term model:
- From Kevin and Paul D: Drop 'Created_by' and 'Creation_date', not useful information to import, check original source of information if needed.
Kevin:I would definitely advocate pick-and-choose over include-everything. We are not the maintainers/develops of this ontology, so I don't see why we should be recording the name of the curator responsible for adding a particular term, or precisely when they added it (to give two examples). This ontology is still in the early stages of development, and is likely to change subtly in definition. By capturing only the "core" parts of it, we give ourselves at least a fighting chance of defining a Acedb model that will not have to be changed each time they release a new version of the DO.
- For the 'subset' tag, follow standard procedure across models:
?DO_term Type GOLD gram-negative_bacterial_infectious_disease gram-positive_bacterial_infectious_disease sexually_transmitted_infectious_disease tick-borne_infectious_disease zoonotic_infectious_disease
- Relationships--Could we also modify the Relationship section as the proposed tag names are new and relationships are used in multiple other classes, could you copy one of the other models as I just created some test data and had the relationship reversed because of the tag names and I wasn't being careful. We should try and re-use common tag structures, that was if there are enough of them we can move them into a Hash to simplify the models file.
?Anatomy_term Lineage Parent_term UNIQUE ?Anatomy_term XREF Daughter_term Daughter_term ?Anatomy_term XREF Parent_term ?SO_term Parent Is_a ?SO_term XREF Is Part_of ?SO_term XREF Part Derived_from ?SO_term XREF Derives Member_of ?SO_term XREF Member Child Is ?SO_term XREF Is_a Part ?SO_term XREF Part_of Derives ?SO_term XREF Derived_from Member ?SO_term XREF Member_of ?Cell Lineage Parent UNIQUE ?Cell XREF Daughter Daughter ?Cell XREF Parent ?GO_term Child Instance ?GO_term XREF Instance_of Component ?GO_term XREF Component_of Parent Instance_of ?GO_term XREF Instance Component_of ?GO_term XREF Component
Gene-disease model
?Gene DB_info Database ?Database ?Database_field Text//for pointing to OMIM ortholog and disease 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
Note: The 'Human_disease_relevance' tag is being moved from the 'Structured_description'tag under ?Gene to the 'Disease_info' tag and is renamed as 'Disease_relevance'.
Proposal for expansion of the Gene-Disease model
We currently have Gene-Disease (DO_term) associations, but we don't have any of the supporting data that let us make these connections, e.g. the allele (variation), transgene etc. Further if we want to curate drug/agent effects on disease, would be good to have the context, e.g was the drug used to ameliorate or exacerbate disease phenotypes in the genetic allele, or transgene etc. This would mean curating at the level of the actual experiment that was done. Towards this, we need a 'Disease_model_annotation' object (similar to the GO_annotation object) to capture all these additional details and tie them all together in a meaningful way, so we can encapsulate all the data related to a single gene-disease model.
Data we want to capture for each model:
- Disease (DO_term)
- Model type: Inducible, Genetic, Transgenic; the genetic and transgenic models can be inducible (heat, chemical etc).
- Strain
- Transgene
- Molecule: Drug, chemical, herb, some compound; whether it ameliorates or exacerbates
For modeling data where the native gene is the experimental model:
?Gene Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence Experimental_model_annotation ?Experimental_model_annotation XREF Gene Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence Disease_relevance ?Text ?Species #Evidence ?Experimental_model_annotation //this is a new class to encapsulate all the annotation details of one model Gene UNIQUE ?Gene XREF Experimental_model_annotation DO_term UNIQUE ?DO_term XREF Experimental_model_annotation Evidence_code UNIQUE ?ECO_term //when we import the ECO, GO_code for now Modeled_with Variation ?Variation Strain ?Strain Transgene ?Transgene Causative_gene ?Gene Phenotype ?Phenotype Disease_phenotype ?Text //for phenotype not represented in WB PO Effective_gene Ameliorating_gene ?Gene Ameliorating_gene_description ?Text //eg. Overexpression Exacerbating_gene ?Gene Exacerbating_gene_description ?Text Effective_molecule Ameliorating_molecule ?Molecule Ameliorated_phenotype ?Phenotype Ameliorated_disease_phenotype ?Text //for phenotype not in WB PO Exacerbating_molecule ?Molecule Exacerbated_phenotype ?Phenotype Exacerbated_disease_phenotype ?Text //for phenotype not in WB PO
DO_term model
Note: Kevin, 12/17/12: Acedb does not accept dashes, so these were converted to underscores for all the tags under the 'Type' tag. Also, first letter of the tag name was capitalized.
?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
Proposal for expansion of the DO_term model
?Disease_model_annotation class
Gene ?Gene Disease UNIQUE ?DO_term XREF Disease_model_annotation Reference UNIQUE ?Paper XREF Disease_model_annotation Variation ?Variation XREF
For modeling data where transgenes are used, usually human transgene, so cannot be attached to a WBGene:
?DO_term Attribute_of Gene_by_biology ?Gene XREF Experimental_model Disease_model_annotation ?Disease_model_annotation XREF Disease//New tag Gene_by_orthology ?Gene XREF Potential_model Phenotype ?Phenotype XREF DO_term WBProcess ?WBProcess XREF DO_term Reference ?Paper XREF DO_term ?Disease_model_annotation class Gene ?Gene Disease UNIQUE ?DO_term XREF Disease_model_annotation Reference UNIQUE ?Paper XREF Disease_model_annotation Variation ?Variation XREF
Changes to expand the Disease Term OA
Fields:
- DO term
- Curator
- Curator history
- New field: Model_type: Experimental, Predicted, NOT_model (could be Experimental by default)
- Variation
- Change required: Transgene *change to multivalue
- New filed: Strain: should be multivalue autocomplete strain drop-down.
- Disease phenotype
- Disease phenotype comment *New (free text field)
- Species
- New field: Evidence code: will be the GO codes for now (single value drop-down)
- Worm model description
- Paper
- Last updated
- Comment (free text field)
- pgid
- Change required: Molecule type: Name change possible? If so have: Exacerbates, Ameliorates, Toxic, *Add Does_not_exacerbate, Does_not_ameliorate, Not_toxic
- Molecule (autocomplete drop-down, WB molecule ontology)
- New field: Other treatment:(free text field for now)
- Affected phenotype: (WB Phenotype Ontology field)
- New field: Affected phenotype comment:(free text field)
Older versions
In order to link alleles/variations, transgenes to DO_term:
?DO_term Worm_disease_model ?Text ?Species #Evidence //big text description elegans model added Jan 2014, for WS242 Disease_model_variation ?Variation ?Phenotype #Evidence //variation and its phenotype, addresses phenologs Disease_model_transgene ?Transgene ?Phenotype #Evidence //transgene used in disease model Molecule_interaction Exacerbated_by_molecule ?Molecule XREF DO_term #molecule_interaction_info Therapeutic_molecule ?Molecule XREF DO_term #molecule_interaction_info ?Molecule_interaction_info Paper_evidence ?Paper Curator_confirmed ?Person Molecule_Type ?Text #Evidence //Metal, Drug, Pesticide, Plant medicinal compound, spice etc Interacts_with_variation ?Variation #Evidence Interacts_with_gene ?Gene #Evidence Exacerbates_phenotype ?Phenotype #Evidence Ameliorates_phenotype ?Phenotype #Evidence Restores_process ?GO_term #Evidence Restores_process ?WBProcess #Evidence Remark ?Text #Evidence Alternate model (no way to keep all molecule-related information together) Molecule interaction Exacerbated_by_molecule ?Molecule XREF DO_term ?GO_term #Evidence Exacerbated_by_molecule ?Molecule XREF DO_term ?WB_Process #Evidence Exacerbated_by_molecule ?Molecule XREF DO_term ?Phenotype #Evidence Therapeutic_molecule ?Molecule XREF DO_term ?GO_term #Evidence Therapeutic_molecule ?Molecule XREF DO_term ?WBProcess #Evidence Therapeutic_molecule ?Molecule XREF DO_term ?Phenotype ?Molecule Exacerbates_disease ?DO_term XREF Exacerbated_by_molecule Therapeutic_for_disease ?DO_term XREF Therapeutic_molecule
Changes to other data models
And we will need to add DO_term tag and object to the Phenotype, WBProcess, Molecule and Reference models.
?Phenotype DO_term ?DO_term #Evidence ?WBProcess DO_term ?DO_term #Evidence ?Paper DO_term ?DO_term #Evidence ?Molecule DO_term ?DO_term #Evidence
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.
Model changes to add reagents to disease
We want to curate Antibodies, Transgenes and Constructs that are used as reagents in papers that model human disease:
?Antibody Antibody_for_disease ?DO_term XREF Associated_antibody #Evidence ?Construct Construct_for_disease ?DO_term XREF Associated_construct #Evidence ?Transgene Transgene_for_disease ?DO_term XREF Associated_transgene #Evidence ?DO_term Reagent_info Associated_antibody ?Antibody XREF Antibody_for_disease Associated_construct ?Construct XREF Construct_for_disease Associated_transgene ?Transgene XREF Transgene_for_disease
Model changes to associate molecule to disease
We want to curate drugs, herbals, metals, organic compounds from papers that either exacerbate or alleviate (are therapeutic for) disease.
?DO term Exacerbated_by_molecule ?Molecule XREF Exacerbates_disease #Exacerbating_molecule_info Alleviated_by_molecule ?Molecule XREF Alleviates_disease #Alleviating_molecule_info We will need to create new Exacerbating_molecule_info and Alleviating_molecule_info classes ?Exacerbating_molecule_info Paper_evidence ?Paper Curator_confirmed ?Person Affected_GO_process ?GO_term Affected_WBProcess ?Process Affected_other_process ?Text Exacerbated_WBphenotype ?Phenotype Exacerbated_other_phenotype ?Text Alleviated_WBphenotype ?Phenotype Alleviated_other_phenotype ?Phenotype Affected_GO_process ?GO_term #Evidence ?Molecule XREF Exacerbates_disease Affected_WBProcess ?WBProcess #Evidence ?Molecule XREF Exacerbates_disease Affected_other_process ?Text #Evidence Alleviated_by_molecule ?Molecule XREF Therapeutic_for_disease Affected_GO_process ?GO_term #Evidence ?Molecule XREF Therapeutic_for_disease Affected_WBProcess ?WBProcess #Evidence ?Molecule XREF Therapeutic_for_disease Affected_other_process ?Text #Evidence ?Molecule Disease_info Exacerbates_disease ?DO_term XREF Exacerbated_by_molecule Therapeutic_for_disease ?DO_term XREF Alleviated_by_molecule
Back To Disease and Drugs
Alternate
Exacerbated_by_molecule ?Molecule XREF Exacerbates_disease Alleviated_by_molecule ?Molecule XREF Therapeutic_for_disease Affected_process Process_exacerbated GO_term ?GO_term #Evidence WBProcess ?WBProcess #Evidence Other ?Text #Evidence Process_alleviated GO_term ?GO_term #Evidence WBProcess ?WBProcess #Evidence Other ?Text #Evidence