Model changes to capture and consolidate human disease data

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Suggestions/Corrections from Hinxton

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

Current version of models

So as of 12/05/2012 we have:

Gene

 ?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
Gene ?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_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 

DO_term

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 


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.
---- 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.

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