ZFIN G2P Association (v2)
The Zebrafish Information Network (ZFIN) is a curated knowledgebase that curates genotype-to-phenotype (G2P) associations from the literature. ZFIN provides the following types of evidence and provenance information for G2P claims:
- The
publicationthat reported evidence used to support the claim. - The
figurefrom this publication that depicts the relevant evidence. - An
evidence codefrom the ECO ontology indicating the type of this evidence. - Key
reagentsused in experiments generating evidence (e.g. morpholinos, DNA constructs)
The example Assertion here states that "The ndr2tf219/tf219;shhaDf(Chr07)t4/Df(Chr07)t4 genotype causes a decreased size otolith phenotype." This Assertion was made by a ZFIN curator based on evidence reviewed from a single publication reporting morphological assays showing the ears of zebrafish with this genotype to have abnormally small auditory otic vesicles relative to wild-type fish.
| Metadata Type | Description | Example Value | SEPIO Representation |
|---|---|---|---|
| Agent | the agent making the assertion | ZFIN organization | linked directly from Assertion node |
| Evidence Code | an evidence class from the ECO Ontology | ECO:0000059 ('experimental evidence') | the ECO class is used to type an Evidence Line individual |
| Figure | a figure holding data used as evidence | ZDB-FIG-100402-3 (Figure 7 from Hammond et al. 2003) | an Evidence Item that supports an Evidence Line |
| Publication | a journal article that reports evidence and its provenance | PMID:12588855 (Hammond et al .2003) | a supporting reference for the Evidence Line, that describes the evidence |
This example is taken from an OWL representation of ZFIN data created by the Monarch Initiative. Each node is an instance (OWL individual) with its IRI and (optional) label shown in bold, and its type IRI and label in regular text below. IRIs are shown as compact CURIEs, whose prefix expansions are shown below. IRIs are based on existing identifier systems where possible (e.g. PMID, ZFIN).
Where no such identifiers exist for a node, it is treated as an anonymous individual (i.e. 'blank node'), or given a hash-based IRI in the Monarch namespace.
Prefix Expansions:
MONARCH: http://www.monarchinitiative.org/MONARCH_
SEPIO: http://purl.obolibrary.org/obo/SEPIO_
DC: http://purl.org/dc/elements/1.1/
SIO: http://semanticscience.org/resource/SIO_
PMID: http://www.ncbi.nlm.nih.gov/pubmed/
A Note on Assertion Semantics: The meaning of the Assertion in the graph above is described only in a free-text annotation, but various approaches can be taken to formally represent Assertion semantics. SEPIO leaves such modeling choices to the implementer. In the Monarch Initiative dataset, Assertion semantics are represented using the OBAN model, which reifies an RDF triple that formally expresses the meaning expressed in an Assertion as a node in the graph. The node, which OBAN calls an 'Association', represents a Proposition can be linked to any number of Assertions that put it forth, and to any number of Evidence Lines that support or refute it. See the page [here] for further discussion of this topic, including a depiction of how Monarch uses SEPIO and OBAN models to formalize the semantics of the ZFIN Assertion above.