ZFIN G2P Association

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 provenance and evidence information for G2P claims:

• An ECO code indicating the type of evidence used to support the claim.
• The publication that reported the curated evidence.
• The figure from this publication that reports relevant evidence.
• Key reagents used in experiments that generated evidence (e.g. morpholinos, DNA constructs)

This ZFIN example is provided to illustrate how SEPIO concisely represents minimal evidence and provenance information that is reported by the majority of curated knowledgebases. Subsequent examples will highlight how the SEPIO model ensures that such simple representations are interoperable with much richer and more complex accounts of evidence and provenance provided by some data sources.

Our exemplar Assertion states that "The ndr2^tf219/tf219;shha^{Df(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.

In the SEPIO model, the Assertion is supported by one Evidence Line typed as an instance of the 'experimental evidence' ECO class. The cited figure represents an Evidence Item supporting this Evidence Line, and the curated publication is a supporting reference that describes this evidence.

Graph Description:

• The RDF data depicted above was created by the Monarch Initiative ETL pipeline.
• Each node in the graph represents an instance (i.e. an OWL individual) with its IRI (and a label where applicable) shown in bold, and its type IRI and label shown non-bolded below.
• IRIs are shown as compact CURIEs (link), whose prefix expansions are shown below.
• Instance 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/

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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.