Model changes to capture and consolidate human disease data

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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.
---- snippet taken from their FAQ ----

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:

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.

New class: Disease_model_annotation and related changes, Feb 2017

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

  1. Add new tag: Modifier_qualifier NOT
  2. Add new tag under Annotation_made_with: Interacting_gene ?Gene
  3. 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        // genetic entity that
                                                                                                  models the disease
                                     Variation UNIQUE ?Variation XREF Disease_model_annotation  // genetic entity that                                                                                                                                     
                                                                                                  models the disease
                                     Transgene UNIQUE ?Transgene XREF Disease_model_annotation  // genetic entity that
                                                                                                  models the disease
                                     Disease_relevant_gene UNIQUE ?Gene XREF Disease_model_annotation//when the
                                                                                                    genetic entity is a gene
                         
                           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
                          
                          Inferred_gene     ?Gene XREF  Disease_model_annotation //to indicate the gene in Variation or
                                                                                       Strain, when the authors tell us
                          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                                  //to indicate that a disease is NOT modeled by the genetic object
                          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 to match 'Modifer qualifier' of AGR data model.
                          

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"

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_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

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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