Kino evaluations

Kino (Kino Enterprise) Usecases

1. Biology oriented Web service annotation and retrieval: Many organizations, such as the DNA Data Bank of Japan (DDBJ), provide service interfaces for biological data retrieval tasks (such as Gene prediction). Biologists typically search and browse through a service catalog such as BioCatalogue and import the relevant service descriptions to a composer tool. Biologist would have to use descriptive terms to extract the most suitable services. Often these terms are imprecise, and several attempts are needed to get to the exact service required for the task at hand.
2. Scientific Document annotation: The scientists at Sanger Institute perform document annotation through a labor intensive process. This is the process in the Figure 1.

Figure 1: Current document annotation workflow at Sanger Institute in UK. Annotators add notes to the document and curators later enhance them manually. This happens in a cycle until the annotations reach the required quality

Empirical Evaluation

Case 1: Improve in Recall

In the case of the Web service retrieval, we observed that BioCatalogue returns about 75 Web services for the search term gene prediction. However, it returns only 20 Web services for the term gene finding, even though gene prediction and gene finding are synonyms. Some of these commonly available synonyms that Kino managed to automatically add as synonyms are available online . The essence of these observations is that such synonyms and cross references have been added to existing ontologies with significant effort and investment; although, the lack of integration leads to underutilizing these resources. Ability to use these synonyms and possibly other details from the ontology improves recall.

Concept Label	Available Synonyms	Reference Concept Id *
Gene finding	Gene prediction	EDAM:0000109
Homology Modeling	Comparative modeling	EDAM:0000175
nucleic acid sequence analysis	nucleotide sequence analysis	EDAM:0000096
sequence alignment	sequence comparison	EDAM:0000182
genetic mapping	genetic linkage, linkage Mapping	EDAM:0000109

Case 2: Convenience from the use of the browser plugin

By using the browser plugin, an alternate workflow for the cumbersome document annotation process was introduced. This is depicted in Figure 2.

Figure 2: The suggested workflow for Sanger which uses the browser plugin to directly embed ontology annotations. The separate manual lookups are avoided, saving significant time and effort.