Data Repository and Data Services

One of the chief objectives of the Phenoscape project is to present a centralized repository to store annotations entered by ichthyologists. These annotations can be queried from a user interface and used to answer Driving_Research_Questions and for Advanced Phenoscape_use_cases. The following tools which are under various stages of development, will serve to realize this objective.

Phenoscape Data loader

A data loader application to refresh the data in the Phenoscape database on a daily basis is under development. The application is being developed as a Perl module, which in sequential order:

Downloads curated NeXML files from the Phenoscape SVN repositories
- Ichthyologists curate scientific publications using the Phenex character matrix annotator and these curations are stored in an SVN repository. The data loader downloads these data files on a daily basis for subsequent uploading into the relational database
Drops and recreates the database
Loads the requisite ontologies into the database
- The annotations of character matrices use terms that are defined in life science ontologies. These ontologies include the Teleost Taxonomy Ontology (TTO), the Relations Ontology, the Teleost Anatomy Ontology (TAO), and the Phenotype and Trait Ontology (PATO). The data loader loads all these definitions into the relational database
Loads the data from the curated NeXML files into the database,
- The data loader transforms the curated data from NeXML syntax to a set of relational tuples (records), which are then sequentially inserted into the database
Invokes the OBD reasoner to elicit implicit information from the data and adds them to the database
- The OBD reasoner uses definitions of transitive relations, relation hierarchies, and relation compositions to infer implicit information. These inferences are added to the relational database in the final step
Logs incomplete annotations into a log file
- The data loader does not load incomplete annotations from the NeXML files into the database. Incomplete annotations contain null values for taxa or phenotype or both. Instead, it logs these incomplete annotations on a file-specific basis in this Problem Log Format. Curators can then work on finishing these annotations which will be subsequently loaded into the database in the next execution of the data loader.

For status updates

Cartik's notes on the Phenoscape Data Loader

For code specific details

OBD API Documentation
- Specific details of OBD related classes and interfaces as documented by Cartik Kothari. These will be updated very often and are meant to be used as an addendum to the The OBOEdit Javadoc

OBD Reasoner

This section documents the inherited code in Perl and embedded SQL, that extracts implicit inferences from the downloaded ontologies and annotations of ZFIN and Phenoscape phenotypes.

Relationships Used

Transitive Relationships (A R B, B R C => A R C)

Transitive relationships are the simplest inferences to be extracted and comprise the majority of new assertions added by the reasoner. Transitive relationships include (ontology in brackets):

is_a (OBO Relations)
has_part (OBO Relations)
part_of (OBO Relations)
integral_part_of (OBO Relations)
has_integral_part (OBO Relations)
proper_part_of (OBO Relations)
has_proper_part (OBO Relations)
improper_part_of (OBO Relations)
has_improper_part (OBO Relations)
location_of (OBO Relations)
located_in (OBO Relations)
derives_from (OBO Relations)
derived_into (OBO Relations)
precedes (OBO Relations)
preceded_by (OBO Relations)
develops_from (Zebrafish Anatomy)
anterior_to (Spatial Ontology)
posterior_to (Spatial Ontology)
proximal_to (Spatial Ontology)
distal_to (Spatial Ontology)
dorsal_to (Spatial Ontology)
ventral_to (Spatial Ontology)
surrounds (Spatial Ontology)
surrounded_by (Spatial Ontology)
superficial_to (Spatial Ontology)
deep_to (Spatial Ontology)
left_of (Spatial Ontology)
right_of (Spatial Ontology)
complete_evidence_for_feature(Sequence Ontology)
evidence_for_feature (Sequence Ontology)
derives_from (Sequence Ontology)
member_of (Sequence Ontology)
exhibits (Phenoscape Ontology)

Relation (role) compositions

Relation (role) compositions are of the form A R1 B, B R2 C => A (R1|R2) C. For example, given A is_a B and B part_of C then A part_of C. The reasoner extracts such inferences and adds them to the database. Specifically, the following relation composition templates are used:

A is_a B, B R C => A R C, where R can be any relation
A R B, B is_a C => A R C, where R can be any relation
Reflexive relations (A is_a A)
Sub relations A R B, R is_a R2 => A R2 B
- An example: If A father_of B and father_of is_a parent_of, then A parent_of B
Relation chains
- Relation chains are a special case of relation composition. Component relations are accumulated into an assembly relation. Specifically, instances of

the relation inheres_in_part_of are accumulated from instances of the relations of inheres_in and part_of. IF A inheres_in B and B part_of C, THEN A inheres_in_part_of C

Intersection Relations

Phenotype annotations are typically "post-composed", where an entity and quality are combined into a Compositional Description. For example, an annotation about the quality decreased size (PATO:0000587) of the entity Dorsal Fin (TAO:0001173) may be post-composed into a Compositional Description that looks like PATO:0000587^OBO_REL:inheres_in(TAO:0001173). Instances of is_a and inheres_in relations are extracted from post compositions like this. In the above example, the reasoner extracts:

PATO:0000587^OBO_REL:inheres_in(TAO:0001173) OBO_REL:inheres_in TAO:0001173, and
PATO:0000587^OBO_REL:inheres_in(TAO:0001173) OBO_REL:is_a PATO:0000587

Sweeps

A reasoner functions over several sweeps. In each sweep, new implicit inferences are derived from the explicit annotations (as described in the previous sections) and added to the database. In the following sweep, inferences added from the previous sweep are used to extract further inferences. This process continues until no additional inferences are added in a sweep. This is when the deductive closure of the inference procedure is reached. No further inferences are possible and the reasoner exits.

Web services

Each service may support multiple media types. The desired media type can be specified by appending ?media=json or similar to the request URL. URI specifications are defined (loosely) using URI Templates.

Term info

URI

<BASE URI>/term/{term_id}

Returns

JSON: <javascript> {

   "id" : "TAO:0001700",
   "name" : "caudal-fin stay",
   "definition" : "Bone that is located anterior to the caudal procurrent rays. Caudal fin stays are unpaired bone.",
   "parents" :
   [
       {
           "relation" : {
               "id" : "OBO_REL:is_a",
               "name" : "is_a"
           },
           "target" : {
               "id" : "TAO:0001514",
               "name" : "bone"
           }

       },
       {
           "relation" : {
               "id" : "OBO_REL:part_of",
               "name" : "part_of"
           },
           "target" : {
               "id" : "TAO:0000862",
               "name" : "caudal fin skeleton"
           }
       }
   ],
   "children" : [] // if there are children, this content should be in the same format as the parents list

} // how should xrefs, etc. be represented, property_value definitions? </javascript>

OWL-RDF:

Todo...

Error

If there is no term with the given ID, the service should return "404 Not Found".

Handling of anonymous post-compositions

Autocomplete

URI

<BASE URI>/term/search?text=[input]&name=[true|false]&syn=[true|false]&def=[true|false]&ontology=[ont1,ont2,...]&limit=[count]

All URI parameters are optional except for text. Default values are name=true, syn=false, def=false. The "ontology" parameter should be a comma-separated list of ontology prefixes to search within. If not given, the default is to search all ontologies. Specifying "ZFIN" for the ontology should be a search for gene nodes, by gene name. The "limit" parameter limits the number of results to the given integer.

Returns

JSON: <javascript> {

   "matches" : [
       {   // overall format
           "id" : "TAO:0001514",
           "name" : "bone",
           "match_type" : "name" | "syn" | "def",
           "match_text" : "this is the term name, synonym name, or definition that matched"
       },
       {   // a name example
           "id" : "TAO:0001514",
           "name" : "bone",
           "match_type" : "name",
           "match_text" : "bone"
       },
       {   // a synonym example
           "id" : "TAO:0001795",
           "name" : "ceratohyal foramen",
           "match_type" : "syn",
           "match_text" : "bericiform foramen"
       },
       {   // a definition example
           "id" : "TAO:0000488",
           "name" : "ceratobranchial bone",
           "match_type" : "def",
           "match_text" : "Ceratobranchials are bilaterally paired cartilage bones that form part of the ventral branchial arches. They articulate medially with the hypobranchials and laterally and dorsally with the epibranchials.  Ceratobranchials 1-5 ossify in the ceratobranchial cartilages."
       }
   ],
   "search_term" : "bone",
   "total" : 1859

} </javascript>

Error

If there are no terms matching the given input, a document should still be returned, containing an empty results list.

Anatomy search summary

URI

<BASE URI>/phenotypes/summary/anatomy/{term_id}

term_id is an anatomy search term. This service returns a summary of all the phenotype annotations involving that anatomy term (or its descendants, via reasoning). The summary is grouped by quality attribute term - all annotations with qualities descending from the same closest attribute should be grouped into the same count.

Returns

JSON: <javascript> {

   "term" : { "id" : "TAO:xxxxx", "name" : "some anatomical part"},
   "qualities" : [
       {
           "id" : "PATO:000xxxxx",
           "name" : "shape",
           "taxon_annotations" : {
               "annotation_count": 5,
               "taxon_count" : 3
           },
           "genotype_annotations" : {
               "annotation_count" : 3,
               "genotype_count" : 2
           }
       },
       {
           // another quality attribute
       } // etc.
   ]

} </javascript>

Anatomy taxon annotations results

URI

<BASE URI>/phenotypes/anatomy/{anatomy_term_id}/taxa/{quality_term_id}?attribute=[true|false]

anatomy_term_id is an anatomy search term. This service returns all of the phenotype annotations involving that anatomy term (or its descendants, via reasoning) and the given quality term (or its descendants, via reasoning). In the result, the values of the outer "entity" and "quality" keys are the search inputs.

The "attribute" query parameter is optional - if "true", the service should first find the corresponding attribute for the given quality, and use that in the search instead of the given quality. The default should be "false".

Returns

JSON: <javascript> {

   "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
   "quality" : { "id" : "PATO:1234", "name" : "some attribute quality"},
   "annotations" : [
   {
       "taxon" : { "id" : "TTO:34242", "name" : "some species" },
       "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
       "quality" : { "id" : "PATO:34242", "name" : "some quality" }
   },
   {
       "taxon" : { "id" : "TTO:34242", "name" : "some species" },
       "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
       "quality" : { "id" : "PATO:34242", "name" : "some quality" }
   },
   {
       "taxon" : { "id" : "TTO:34242", "name" : "some species" },
       "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
       "quality" : { "id" : "PATO:34242", "name" : "some quality" }
   }
   ]

} </javascript>

Anatomy genotypes annotations results

URI

<BASE URI>/phenotypes/anatomy/{anatomy_term_id}/genes/{quality_term_id}

anatomy_term_id is an anatomy search term. This service returns all of the phenotype annotations for genotypes involving that anatomy term (or its descendants, via reasoning) and the given quality term (or its descendants, via reasoning). In the result, the values of the outer "entity" and "quality" keys are the search inputs.

The "attribute" query parameter is optional - if "true", the service should first find the corresponding attribute for the given quality, and use that in the search instead of the given quality. The default should be "false".

Returns

JSON: <javascript> {

   "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
   "quality" : { "id" : "PATO:1234", "name" : "some attribute quality"},
   "annotations" : [
         {
           "genotype" : { "id" : "ZFIN:34242", "name" : "some genotype" },
           "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" }
       },
       {
           "genotype" : { "id" : "ZFIN:34242", "name" : "some genotype" },
           "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" }
       },
       {
           "genotype" : { "id" : "ZFIN:34242", "name" : "some genotype" },
           "entity" : { "id" : "TAO:34242", "name" : "some anatomical part" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" }
       }
   ]

} </javascript>

Gene search summary

URI

<BASE URI>/phenotypes/summary/gene/{term_id}

term_id is an gene symbol search id. This service returns all the phenotype annotations involving that gene. Identical annotations from different genotypes are lumped together. Each annotation has a list of all the genotypes which exhibited it. Each annotation includes the term from TAO matching the ZFA term in "teleost_entity".

Returns

JSON: <javascript> {

   "gene" : { "id" : "ZFIN:xxxxx", "name" : "some gene name"},
   "annotations" : [
       {
           "entity" : { "id" : "ZFA:34242", "name" : "some anatomical part" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" },
           "teleost_entity" : { "id" : "TAO:34242", "name" : "some anatomical part" }
           "genotypes" : [
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" },
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" },
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" }
           ]
       },
       {
           "entity" : { "id" : "ZFA:34242", "name" : "some anatomical part" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" },
           "teleost_entity" : { "id" : "TAO:34242", "name" : "some anatomical part" }
           "genotypes" : [
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" },
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" },
               { "id" : "ZFIN:xxxxx", "name" : "some genotype" }
           ]
       }
   ]

} </javascript>

Data Repository and Data Services

Contents

Phenoscape Data loader

OBD Reasoner

Relationships Used

Sweeps

Web services

Term info

Handling of anonymous post-compositions

Autocomplete

Anatomy search summary

Anatomy taxon annotations results

Anatomy genotypes annotations results

Gene search summary

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