scilink api.md

SciLink

https://docs.google.com/document/d/136NBEwqi0Jwon4h23m0BfDMMIn_TBx06o1pPXNz8HXk/edit

This API wraps a number of different more modular APIs and database engines or analysis services. The idea is that the API implementation will do the right thing - for example, using Solr for searches but injecting results with fast in-memory traversal of ontology graphs.

When starting up, configure with:

• PURL of tbox
• BOLT connector metadata for neo4j
• SPARQL endpoints

OWL

Can we just compose owlery here?

• Wraps: OWLAPI/scowl/owlery

e.g.

Subclasses [/kbs/{kb}/subclasses{?object,prefixes,direct}]

Graph

This provides access over the full contents of all knowledge bases, with a graph level of abstraction

• Wraps: neo4j OR sparql OR in-memory

Entity Search

lots of common fields

Autocomplete [/search/autocomplete{?searchTerms,?negatedSearchTerms,selectFields,facetFields,categories}]

• Wraps: Solr

Lexical Search [/search/lexical{?searchTerms,?negatedSearchTerms,selectFields,facetFields,categories}]

• Wraps: Solr

Ontology Entity Search [/search/ont{?searchTerms,?negatedSearchTerms,selectFields,facetFields,categories,includeEntailed,isFuzzy}]

• Wraps: Solr (bool)
• Wraps: owlsim3 (fuzzy) - or compositio of solr->sim

Link Search [/search/link{?searchTerms,?negatedSearchTerms,selectFields,facetFields,subjCategories,objCategories,includeEntailed,isFuzzy}]

Textual Annotation

Operations involving recognizing and interpreting entities in text

Groupings

Operations on groups of entities

Resolution [/set/resolve{?entities,ontologies,species,type}]

Given a list of entity designators (e.g. gene symbols) resolve these to indentifiers

Enrichment [/set/enrichment{?entities,ontologies}]

Find enriched ontology classes or entity sets based on an input entity set

• Wraps: owlsim3

Paths

What Connects? [/path/paths{?entities}]

• Wraps: owlsim3 OR neo4j

How are the entities connected? Typically called with 2 entities.

Different implementations may do different kinds of things. E.g. path in sequence space, ontology space, graph path, ..

SPARQL

Simple sparql wrapper - required?

• Wraps: SPARQL

Analytics

Who has queried for what?

Genes

Convenience methods

Resolve Gene [/gene/{id}]

Map an ID

Fetch Gene [/gene/{id}]

Fetch Orthologs [/gene/ortholog/{id}]

Fetch Associatios [/gene/associatios/{id}]

Fetch Phenotypes [/gene/phenotype/{id}]

Gene Query [/gene/query/{class, species}]

Genotypes

Resolve Genotype [/genotype/{id}]

Map an ID

Fetch Genotype [/genotype/{id}]

Fetch Alleles [/genotype/alleles/{id}]

Fetch Phenotypes [/genotype/phenotype/{id}]

Genotype Query [/genotype/query/{class, species}]

The implementation will use a variety of different engines depending on the task at hand (e.g. solr for faceted or textual search, or for retrieval of associations; owlsim for noisy search; OWLAPI or triplestore or neo4j for ontology operations). This will be transparent to the user.

The implementation will be in Scala. This will allow direct JVM access where required, obviating the need for complex and inefficient chaining of web apis. The initial implementation may be a port of scigraph-services to scala, and can be extended.