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

From WormBaseWiki
Jump to navigationJump to search
Line 377: Line 377:
 
   Associated_transgene ?Transgene XREF      Transgene_for_disease
 
   Associated_transgene ?Transgene XREF      Transgene_for_disease
 
</pre>
 
</pre>
 
==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.
 
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
?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
 
             
 
</pre>
 
Back To [[Disease and Drugs]]
 
 
Alternate
 
<pre>
 
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
 
</pre>
 
 
  
 
== Disease_model_annotation New Class==
 
== Disease_model_annotation New Class==

Revision as of 18:49, 9 February 2017

Gene-disease model discussion

Paul D's suggestions/corrections for the 'Disease_info' tag under ?Gene::

  • Add ?Species tag instead of 'Experimental_model_for_human' type tags, to indicate species information.

Suggestions/Corrections for the ?DO_term model:

  • From Kevin and Paul D: Drop 'Created_by' and 'Creation_date', not useful information to import, check original source of information if needed.

Kevin:I would definitely advocate pick-and-choose over include-everything. We are not the maintainers/develops of this ontology, so I don't see why we should be recording the name of the curator responsible for adding a particular term, or precisely when they added it (to give two examples). This ontology is still in the early stages of development, and is likely to change subtly in definition. By capturing only the "core" parts of it, we give ourselves at least a fighting chance of defining a Acedb model that will not have to be changed each time they release a new version of the DO.

  • For the 'subset' tag, follow standard procedure across models:
?DO_term
Type       GOLD
           gram-negative_bacterial_infectious_disease
           gram-positive_bacterial_infectious_disease
           sexually_transmitted_infectious_disease
           tick-borne_infectious_disease
           zoonotic_infectious_disease


  • Relationships--Could we also modify the Relationship section as the proposed tag names are new and relationships are used in multiple other classes, could you copy one of the other models as I just created some test data and had the relationship reversed because of the tag names and I wasn't being careful. We should try and re-use common tag structures, that was if there are enough of them we can move them into a Hash to simplify the models file.
 ?Anatomy_term
 Lineage      Parent_term  UNIQUE  ?Anatomy_term XREF Daughter_term
              Daughter_term        ?Anatomy_term XREF Parent_term
 ?SO_term
         Parent Is_a ?SO_term XREF Is
                Part_of ?SO_term XREF Part
                Derived_from ?SO_term XREF Derives
                Member_of ?SO_term XREF Member
         Child  Is ?SO_term XREF Is_a
                Part ?SO_term XREF Part_of
                Derives ?SO_term XREF Derived_from
                Member ?SO_term XREF Member_of
 ?Cell
        Lineage Parent  UNIQUE  ?Cell XREF Daughter
                Daughter        ?Cell XREF Parent
 ?GO_term
        Child     Instance ?GO_term XREF Instance_of
                  Component ?GO_term XREF Component_of
        Parent    Instance_of ?GO_term XREF Instance
                  Component_of ?GO_term XREF Component

Gene-disease model

 ?Gene
 DB_info  Database ?Database ?Database_field Text//for pointing to OMIM ortholog and disease
 Disease_info 	Experimental_model ?DO_term XREF Gene_by_biology   ?Species   #Evidence	            
              	Potential_model	   ?DO_term XREF Gene_by_orthology ?Species #Evidence
              	Disease_relevance  ?Text ?Species #Evidence

Note: The 'Human_disease_relevance' tag is being moved from the 'Structured_description'tag under ?Gene to the 'Disease_info' tag and is renamed as 'Disease_relevance'.

Changes to expand the Gene-Disease OA

  1. WBGene
  2. Curator
  3. Curator History
  4. Experimental Model for
  5. Variation
  6. New Strain: WB Strain list, multi value ontology
  7. New Other Strain (free-text): to hold a non-WB strain until it becomes one.
  8. Disease phenotype
  9. New Disease phenotype comment (free big text)
  10. ChangeTransgene to Interacting Transgene (multi-choice WB transgene list): a transgene is introduced in addition to the genetic mutation that is the disease model. See WBPaper00039877: unc-29(e193)+ Abeta expressing transgene
  11. Paper for Exp Mod
  12. OMIM disease for Exp Mod
  13. Last updated for Exp Mod
  14. Species
  15. Disease relevance
  16. Paper for disease relevance
  17. OMIM disease for Disease Rel
  18. OMIM gene for Disease Rel
  19. Last Updated for Disease Rel
  20. Comment
  21. pgid
  22. Molecule Type
  23. Molecule
  24. New Other treatment (free text): free text field for now, use for other non-molecule treatments such as radiation etc.
  25. Affected Phenotype
  26. New Affected Phenotype comment: free text field
  27. New Molecule 2: (single value, WB molecule ontology) When there is a second molecule treatment together with the first one.
  28. New Affected phenotype comment 2 (free text field): To explain either exacerbation or amelioration of the phenotype caused by the first molecule, by the second molecule, or no effect.

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


Changes to expand the Disease Term OA

Each row in this OA should represent one experiment, which is considered as one model. Fields: Lines with 'New' or 'Change' in bold are being considered.

  1. DO term
  2. Curator
  3. Curator history
  4. Model_type: Experimental, Predicted, NOT_model (could be Experimental by default)
  5. Variation: multivalue
  6. Transgene: together with Strain and Variation, and change to multivalue
  7. Strain: multivalue autocomplete strain drop-down.
  8. New Other strain (free text): to hold a non-WB strain until it becomes one.
  9. Disease phenotype, multi-value ontology
  10. Disease phenotype comment (free text field)
  11. Species
  12. Evidence code: will be the GO codes for now (single value drop-down)
  13. Worm model description
  14. Paper
  15. OMIM disease: will be OMIM ids, so multivalue, comma separated
  16. OMIM gene: will be OMIM ids, so mulitvalue, comma separated
  17. Last updated
  18. Comment (free text field)
  19. pgid

Have a heading for this section of the OA, call it 'Treatment'.

#Change Molecule type to Treatment Type: Exacerbates, Ameliorates, Toxic, No effect, Does_not_exacerbate, Does_not_ameliorate, Not_toxic (These qualifiers will be used to the entire treatment whether to 1 or 2 or 3 treatments together, or should these be to each treatment individually)

# Change Molecule to Molecule 1(autocomplete drop-down, WB molecule ontology)

  1. Other treatment 1:free text field for now, use for other non-moleucle treatments such as radiation etc.
  2. Affected phenotype: WB Phenotype Ontology field, multivalue
  3. Affected phenotype comment:free text field, for comments about the affected phenotype

Have a 'Add molecule button', creates field 'Molecule 2' (WB molecule ontology), if pressed again creates field 'Molecule 3' (WB molecule ontology).

If adding molecule fields on the fly is not possibl, will have to have at least 3 molecule fields.

  1. New Molecule 2: (single value, WB molecule ontology) When there is a second molecule treatment together with the first one.
  2. New Affected phenotype comment 2 (free text field): To explain either exacerbation or amelioration of the first molecule caused phenotype by the second molecule, or no effect.

The below fields are still being worked out, will not be added to the OA as yet:

  1. Interacting gene:
  2. Interacting gene effect:
  3. Interacting other gene:
  4. Interacting other gene effect:
  5. Interacting variation:
  6. Interacting variation effect:

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

Disease_model_annotation New Class

Adding the model here as the original was communicated via Word Doc with v.bad formatting




///////////////////////////////////////////////////////////////
//
// ?Disease_model_annotation class - Ranjana WS259
//
////////////////////////////////////////////////////////////////


?Disease_model_annotation Disease_name ?DO_term XREF Disease_model_annotation
                          Modeled_by UNIQUE Strain ?Strain         // genetic entity that models the disease
                                            Variation ?Variation   // genetic entity that models the disease
                                            Transgene ?Transgene   // genetic entity that models the disease
                          Disease_relevant_gene ?Gene XREF  Disease_model_annotation //when the genetic entity is a gene or to indicate the causative gene in the above Strain, 
                          Association_type UNIQUE is_model_of      // All 5 tags describe the relationship between the genetic entity and the disease (condition)
                                                  causes_or_contributes_to_condition
                                                  causes_condition
                                                  contributes_to_condition
                                                  is_marker_for
                          Evidence_code ?GO_code                              // will use ECO later on
                          Qualifier NOT                                       //to indicate that a disease is ~NOT~ modeled by X (to capture negative data)
                          Experimental_condition Inducing_chemical ?Molecule  //to indicate the disease-inducing agent
                                                 Inducing_agent ?Text         //e.g. diet, radiation, temperature or other, not in Molecule class
                          Modifier_info Modifier_transgene ?Transgene //genetic entity that actually modifies the disease
                                        Modifier_variation ?Variation // (same as above)
                                        Modifier_strain ?Strain       // (same as above)
                                        Modifier_gene ?Gene           // to indicate the gene (when authors provide this) in the modifying Transgene, Variation, Strain.
                                        Modifier_molecule ?Molecule   // to indicate chemical modifiers of the disease
                                        Other_modifier ?Text          // to indicate other modifiers of the disease eg., diet, radiation, surgery etc
                          Modifier_association_type UNIQUE condition_ameliorated_by  //to indicate the association type  between modifiers and disease
                                                           condition_exacerbated_by
                          Genetic_sex UNIQUE hermaphrodite   //indicates genetic sex of the disease model
                                             male
                                             female
                          Disease_phenotype_info Disease_phenotype ?Phenotype     // Phenotypes similar to human disease phenotypes
                                                 Ameliorated_phenotype ?Phenotype // Phenotypes that the modifier ameliorates
                                                 Exacerbated_phenotype ?Phenotype // Phenotypes that the modifier exacerbates
                                                 Disease_phenotype_comment ?Text  // To describe affected, ameliorated or exacerbated phenotypes not in WB PO
                          Paper_evidence ?Paper
                          DB_info Database ?Database ?Database_field ?Text //Specifically to indicate the OMIM gene that the worm model corresponds to in manual annotation
                          Curator_confirmed ?Curator
                          Date_last_updated UNIQUE DateType

Preliminary model errors encountered when doing the initial import (corrected above):

1) Duplicate tag Disease_model_annotation in model ?Molecule

Changed to:

                       Disease_model_Inducing ?Disease_model_annotation XREF Inducing_chemical
                       Disease_model_Modifier ?Disease_model_annotation XREF Modifier_molecule

2) Typo in ?Molecule class

                       Modifies_disease ?DO_term XREF Molecule_modifer
                       Modifies_disease ?DO_term XREF Molecule_modifier

3) Not all tags are XREF both ways...is this intentional?