Difference between revisions of "Model changes to capture and consolidate human disease data"

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==Original Model proposals==
+
==Gene class proposal (April 2020)==
A new tag ‘Disease_info’ proposed to consolidate disease-related data in WormBase:
+
*Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Disease_relevant_gene
 +
*Add 3 new tags
  
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?Gene
+
?Gene
DB_info      Database                    ?Database ?Database_field Text
+
Disease_info Experimental_model ?DO_term XREF Gene_by_biology   ?Species  #Evidence              
Disease_info Experimental_model_for_human ?DO_term XREF Gene_by_biology #Evidence              
+
            Potential_model   ?DO_term XREF Gene_by_orthology ?Species #Evidence
              Potential_model_for_human ?DO_term XREF Gene_by_orthology #Evidence
+
            Disease_relevance  ?Text ?Species #Evidence
              Human_disease_relevance ?Text #Evidence //moved from ‘structured description’ tag.
+
            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
 +
 
 
</pre>
 
</pre>
  
Model for Disease Ontology Term:
+
 
 +
==Variation class proposal (April 2020)==
 +
*Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Variation
 +
*Add 3 new tags
 
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?DO_term
+
 
Name  UNIQUE              ?Text
+
?Variation
Status UNIQUE              Valid
+
Disease_info Models_disease ?DO_term XREF Disease_model_variation
                            Obsolete
+
             Modifies_disease ?DO_term  XREF  Disease_modifier_variation //New tag
Alternate_id              ?Text
+
    Models_disease_in_annotation ?Disease_model_annotation XREF  Variation //New tag
Definition UNIQUE          ?Text
+
        Modifies_disease_in_annotation ?Disease_model_annotation XREF  Modifier_variation//New tag
Comment                    Text
 
Synonymn                  ?Text Scope_modifier UNIQUE Broad
 
                                                        Exact
 
                                                        Narrow
 
                                                        Related
 
Relationship      Is_a_child  ?DO_term  XREF  Is_a_parent
 
                  Is_a_parent ?DO_term XREF Is_a_child
 
DB_info          Database    ?Database  ?Database_field  Text              
 
  Replaced_by                    ?DO_term
 
  Subset                        Text                 
 
Created_by                    Text
 
Creation_date                  Text           
 
Attribute_of Gene_by_biology    ?Gene      XREF   DO_term
 
                Gene_by_orthology ?Gene      XREF  DO_term
 
                Phenotype ?Phenotype XREF   DO_term
 
                WBProcess  ?WBProcess XREF  DO_term
 
                Reference ?Paper      XREF  DO_term
 
  Index Ancestor  ?DO_term  XREF Descendent     
 
        Descendent ?DO_term  XREF Ancestor 
 
  Version UNIQUE Text
 
 
</pre>
 
</pre>
  
==Suggestions/Corrections from Hinxton==
+
==Strain class proposal (April 2020)==
 +
*Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Strain
 +
*Add 3 new tags
 +
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'''Paul D's suggestions/corrections for the 'Disease_info' tag under ?Gene::'''
+
?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
 +
</pre>
  
*Add ?Species tag instead of 'Experimental_model_for_human' type tags, to indicate species information.
+
==Genotype class proposal (April 2020)==
 +
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'''Suggestions/Corrections for the ?DO_term model:'''
+
?Genotype
*Drop 'Created_by' and 'Creation_date', not useful information to import, check original source of information if needed.
+
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
 +
</pre>
  
Paul:If there is a genuine reason to capture the complete file then by all means capture the data, it's just when boiling the data down leaves you with some scrap of data that isn't informative I would vote for not incorporating as the raw data is always available in the source file if someone really wants to see it.
+
==Transgene class proposal (April 2020)==
 +
*Remove tag: Disease_model_annotation ?Disease_model_annotation XREF Transgene
 +
*Add 3 new tags
 +
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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.
+
?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
  
*For the 'subset' tag, follow standard procedure across models:
+
</pre>
?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
 
  
Ideally this would have been UNIQUE but there are 178 DO_terms with multiple subset lines populated.
+
==DO_term class proposal (April 2020)==
 +
*5 new tags for WS278
 +
*2 genotype related New tags went in for WS277
 +
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Or is there something better that maintains flexibility but controls the vocabulary better that Text
+
?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    //New tag 
 +
            Disease_modifier_genotype ?Genotype XREF Modifies_disease //New tag
 +
            Chemical_inducer ?Molecule XREF Induces_disease
 +
            Other_inducer  ?Text                                     //New tag
 +
            Molecule_modifier ?Molecule XREF Modifies_disease
 +
           
 +
</pre>
  
Ranjana--If both ?GO_term and ?DO_term were to use 'Subset' and follow this structure, for the sake of uniformity across ontology models, would this be fine or should I switch the tag to 'Type'?
+
====.ace file example====
 +
*Rule for the dumper:For each PGID (not across all PGIDs), if Genotype is present, dump the genotype object only (dis_genotype) and not Gene (dis_wbgene), Variation (dis_variation), Transgene (dis_transgene) or strain (dis_strain)
 +
*The following objects are dumped under the DO_term class:
 +
**Disease relevant gene (dis_wbgene), acedb tag: Gene_by_biology//Add for WS278
 +
**Variation (dis_variation), acedb tag: Disease_model_variation
 +
**Strain (dis_strain), acedb tag: Disease_model_strain
 +
**Transgene (dis_transgene), acedb tag: Disease_model_transgene
 +
**Genotype (dis_genotype), acedb tag: Disease_model_genotype //Add for WS278
 +
**Modifier transgene (dis_modtransgene), acedb tag: Disease_modifier_transgene//Add for WS278
 +
**Modifier variation (dis_modvariation), acedb tag: Disease_modifier_variation//Add for WS278
 +
**Modifier strain (dis_modstrain), acedb tag: Disease_modifier_strain // Add for WS278
 +
**Modifier gene  (dis_modgene), acedb tag: Disease_modifier_gene //Add for WS278
 +
**Modifier genotype (dis_modgenotype), acedb tag: Disease_modifier_genotype //Add for WS278
 +
**Inducing chemical (dis_inducingchemical), acedb tag: Inducing_chemical
 +
**Inducing agent (dis_inducingagent), acedb tag: Other_inducer (free text value) //Add for WS278
 +
**Modifier molecule (dis_modmolecule)
  
*This tag structure isn't workable as there isn't a general DO_term tag in the ?Gene model and it's a 2:1.
 
?DO_term
 
Attribute_of        Gene_by_biology    ?Gene      XREF  DO_term
 
                      Gene_by_orthology  ?Gene      XREF  DO_term
 
*This is also not a permitted tag combination, you aren't allowed to build a branch off a Text/?Text tag, this might be a bug in the acedb code so I have raised a ticket with the acedb dev team, but as of now it's a show stopper, could you re-think this section.
 
 
?DO_term
 
Synonymn ?Text Scope_modifier UNIQUE Broad
 
                                      Exact
 
                                      Narrow
 
                                      Related
 
Would this work?
 
?DO_term
 
  Synonymn UNIQUE Broad  ?Text
 
                  Exact  ?Text
 
                  Narrow  ?Text
 
                  Related ?Text
 
OR
 
?DO_term
 
Synonymn_broad ?Text
 
Synonymn_exact ?Text
 
Synonymn_narrow ?Text
 
Synonymn_related ?Text
 
OR
 
?DO_term
 
Synonymn Broad_synonymn ?Text
 
          Exact_synonymn ?Text
 
          Narrow_synonymn ?Text
 
          Related_synonymn ?Text
 
           
 
 
*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.
 
  
 
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?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
 
  
 +
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
 
</pre>
 
</pre>
  
*Index and Relationship--Are these not storing the same data?
+
==Disease_model_annotation class proposal (April 2020)==
Ranjana--I think Relationship is for the immediate parent/child information, whereas under  Index we would list every ancestor and descendant so as to be able to get the complete ancestory.
+
*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
  
==Current version of models==
 
 
'''So as of 12/05/2012 we have:'''
 
=== Gene ===
 
 
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  ?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            
+
?Disease_model_annotation
              Potential_model   ?DO_term XREF Gene_by_orthology ?Species #Evidence
+
Modeled_by    Strain UNIQUE ?Strain XREF Models_disease_in_annotation ?Text    //Changed XREF
              Disease_relevance ?Text ?Species #Evidence
+
              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
 +
              Genotype UNIQUE ?Genotype XREF Models_disease_in_annotation //Need to dump for WS278
 +
Evidence_code ECO_term ?ECO_term      //new tag
 +
              GO_code ?GO_code        //old tag, but add "GO_code" in front of ?GO_code for WS278
 +
             
 +
 
 +
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_genotype ?Genotype  XREF Modifies_disease_in_annotation //need to dump for WS278
 +
              Modifier_molecule  ?Molecule  XREF Disease_model_modifier
 +
              Other_modifier    ?Text  
 
</pre>
 
</pre>
  
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'.
+
===.ace example for WS278===
 +
Rule for dumper
 +
*For each PGID (not across all PGIDs) if Genotype is present (dis_genotype):
 +
** dump that for the acedb tag "Genotype"; do not dump gene, variation, strain or transgene
 +
**Do not dump any "Interacting xxxx" field (dis_interactxxx) from the OA
 +
*Replace acedb tag "Evidence_code" with "GO_code" for OA field Evidence Code(dis_goinference)
  
=== DO_term ===
 
  
 
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?DO_term
 
Name  UNIQUE               ?Text
 
Status UNIQUE              Valid
 
                            Obsolete
 
Alternate_id               ?Text
 
Definition UNIQUE         ?Text
 
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
 
</pre>
 
  
===Changes to other data models===
+
Disease_model_annotation : "WBDOannot00000290"
 +
Disease_term "DOID:11723"
 +
Disease_of_species "Homo sapiens"
 +
Genotype "WBGenotype00000013"
 +
Inferred_gene "WBGene00001131"
 +
Inferred_gene "WBGene00001248"
 +
Association_type "is_implicated_in"
 +
GO_code "IMP"
 +
Genetic_sex "hermaphrodite"
 +
Paper_evidence "WBPaper00034698"
 +
Database "OMIM" "disease" "310200"
 +
Curator_confirmed "WBPerson324"
 +
Date_last_updated "2018-10-08"
 +
 
  
And we will need to add DO_term tag and object to the Phenotype, WBProcess and Reference models.
+
Disease_model_annotation : "WBDOannot00000623"
  ?Phenotype
+
Disease_term "DOID:5688"
DO_term ?DO_term #Evidence
+
Disease_of_species "Homo sapiens"
 
+
Genotype "WBGenotype00000014"
?WBProcess
+
Inferred_gene "WBGene00003319"
DO_term ?DO_term #Evidence
+
Inferred_gene "WBGene00006944"
+
Association_type "is_implicated_in"
?Paper
+
GO_code "IMP"
DO_term ?DO_term #Evidence
+
Modifier_molecule "WBMol:00005424"
 +
Modifier_association_type "condition_ameliorated_by"
 +
Genetic_sex "hermaphrodite"
 +
Paper_evidence "WBPaper00041652"
 +
Curator_confirmed "WBPerson324"
 +
Date_last_updated "2018-10-25"
  
?Molecule
+
</pre>
DO_term ?DO_term #Evidence 
 
  
 
==Disease Ontology .obo to AceDB tag mapping==
 
==Disease Ontology .obo to AceDB tag mapping==
 +
 +
===Source of files===
  
 
[http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/?sortby=date#dirlist SourceForge] repo of multiple DO files.
 
[http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/?sortby=date#dirlist SourceForge] repo of multiple DO files.
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http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/HumanDO.obo disease ontology .obo file
 
http://diseaseontology.svn.sourceforge.net/viewvc/diseaseontology/trunk/HumanDO.obo disease ontology .obo file
  
 +
===Example obo and .ace formats===
 +
 +
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 +
 +
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"
 +
</pre>
  
 
==Adding Disease Ontology as a ?Database object - DONE==
 
==Adding Disease Ontology as a ?Database object - DONE==
Line 284: Line 380:
  
 
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.
 
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.
 +
 +
== 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====
 +
#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====
 +
<pre>
 +
?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
 +
</pre>
 +
 +
====Sample .ace file====
 +
<pre>
 +
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"
 +
</pre>
 +
 +
====Current Gene class (as relates to disease)====
 +
<pre>
 +
?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
 +
</pre>
 +
 +
====Changes to DO_term class====
 +
<pre>
 +
 +
?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
 +
</pre>
 +
 +
====Current Variation, Strain, Transgene and Molecule classes====
 +
<pre>
 +
?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
 +
</pre>
 +
 +
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.
 +
 +
'''Back To''' [[Disease and Drugs]]

Latest revision as of 20:55, 21 May 2020

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)

  • 5 new tags for WS278
  • 2 genotype related New tags went in for WS277

?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    //New tag   
             Disease_modifier_genotype ?Genotype XREF Modifies_disease //New tag
             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 each PGID (not across all PGIDs), if Genotype is present, dump the genotype object only (dis_genotype) and not Gene (dis_wbgene), Variation (dis_variation), Transgene (dis_transgene) or strain (dis_strain)
  • The following objects are dumped under the DO_term class:
    • Disease relevant gene (dis_wbgene), acedb tag: Gene_by_biology//Add for WS278
    • Variation (dis_variation), acedb tag: Disease_model_variation
    • Strain (dis_strain), acedb tag: Disease_model_strain
    • Transgene (dis_transgene), acedb tag: Disease_model_transgene
    • Genotype (dis_genotype), acedb tag: Disease_model_genotype //Add for WS278
    • Modifier transgene (dis_modtransgene), acedb tag: Disease_modifier_transgene//Add for WS278
    • Modifier variation (dis_modvariation), acedb tag: Disease_modifier_variation//Add for WS278
    • Modifier strain (dis_modstrain), acedb tag: Disease_modifier_strain // Add for WS278
    • Modifier gene (dis_modgene), acedb tag: Disease_modifier_gene //Add for WS278
    • Modifier genotype (dis_modgenotype), acedb tag: Disease_modifier_genotype //Add for WS278
    • Inducing chemical (dis_inducingchemical), acedb tag: Inducing_chemical
    • Inducing agent (dis_inducingagent), acedb tag: Other_inducer (free text value) //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
              Genotype UNIQUE ?Genotype XREF Models_disease_in_annotation //Need to dump for WS278
Evidence_code ECO_term ?ECO_term       //new tag
              GO_code  ?GO_code        //old tag, but add "GO_code" in front of ?GO_code for WS278
              

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_genotype  ?Genotype  XREF Modifies_disease_in_annotation //need to dump for WS278
              Modifier_molecule  ?Molecule  XREF Disease_model_modifier
              Other_modifier     ?Text 

.ace example for WS278

Rule for dumper

  • For each PGID (not across all PGIDs) if Genotype is present (dis_genotype):
    • dump that for the acedb tag "Genotype"; do not dump gene, variation, strain or transgene
    • Do not dump any "Interacting xxxx" field (dis_interactxxx) from the OA
  • Replace acedb tag "Evidence_code" with "GO_code" for OA field Evidence Code(dis_goinference)



Disease_model_annotation : "WBDOannot00000290"
Disease_term	"DOID:11723"
Disease_of_species	"Homo sapiens"
Genotype "WBGenotype00000013"
Inferred_gene	"WBGene00001131"
Inferred_gene	"WBGene00001248"
Association_type	"is_implicated_in"
GO_code	"IMP"
Genetic_sex	"hermaphrodite"
Paper_evidence	"WBPaper00034698"
Database "OMIM" "disease"	"310200"
Curator_confirmed	"WBPerson324"
Date_last_updated	"2018-10-08"


Disease_model_annotation : "WBDOannot00000623"
Disease_term	"DOID:5688"
Disease_of_species	"Homo sapiens"
Genotype  "WBGenotype00000014"
Inferred_gene	"WBGene00003319"
Inferred_gene	"WBGene00006944"
Association_type	"is_implicated_in"
GO_code	"IMP"
Modifier_molecule	"WBMol:00005424"
Modifier_association_type	"condition_ameliorated_by"
Genetic_sex	"hermaphrodite"
Paper_evidence	"WBPaper00041652"
Curator_confirmed	"WBPerson324"
Date_last_updated	"2018-10-25"

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 ?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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