Difference between revisions of "Model changes to capture and consolidate human disease data"
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==DO_term model== | ==DO_term model== |
Revision as of 19:43, 10 February 2017
Contents
- 1 Gene-disease model discussion
- 2 Gene-disease model
- 3 DO_term model
- 4 Disease Ontology .obo to AceDB tag mapping
- 5 Adding Disease Ontology as a ?Database object - DONE
- 6 Linking back to the Disease Ontology
- 7 Disease Ontology Browser REST API
- 8 Disease Data dumping for citace uploads
- 9 Disease_model_annotation, New Class, Feb 2017
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'.
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
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, New Class, Feb 2017
Proposed by Ranjana, Feb, 2017
?Disease_model_annotation Disease_name ?DO_term XREF Disease_model_annotation Modeled_by UNIQUE Strain ?Strain XREF Disease_model_annotation // genetic entity that models the disease Variation ?Variation XREF Disease_model_annotation // genetic entity that models the disease Transgene ?Transgene XREF Disease_model_annotation // genetic entity that models the disease Disease_relevant_gene ?Gene XREF Disease_model_annotation //when the genetic entity is a gene or to indicate the causative gene in the above S, V or T. Association_type UNIQUE is_model_of // All 5 tags describe the relationship between the genetic entity and the disease (condition) causes_or_contributes_to_condition causes_condition contributes_to_condition is_marker_for Evidence_code ?GO_code // will use ECO later on Qualifier NOT //to indicate that a disease is NOT modeled by X 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 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 Disease_phenotype_comment ?Text // To describe non-WPO phenotypes Paper_evidence ?Paper DB_info Database ?Database ?Database_field ?Text //To indicate the OMIM gene manually Curator_confirmed ?Curator Date_last_updated UNIQUE DateType
Changes to Gene class
?Gene 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_name //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
Changes to 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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