Andrew I. Su

Peter W. Rose, Benjamin M. Good, Amanda M. Saravia-Butler et al.

MCP Server Proto-OKN (mcp-proto-okn) is a Python-based Model Context Protocol server that enables AI assistants to discover, inspect, query and integrate scientific knowledge graphs through natural language. The server provides graph routing, schema inspection, SPARQL execution, ontology expansion, multi-graph querying, and transcript generation, lowering the barrier to cross-domain knowledge graph analysis for biomedical and scientific users. mcp-proto-okn is implemented in Python using the FastMCP framework and is available at https://github.com/sbl-sdsc/mcp-proto-okn. Documentation, client configuration instructions, and example analysis transcripts are provided in the GitHub repository.

Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner et al.

Branch is a web application that provides users with no programming with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and evaluating decision trees. These trees can be used to compose and test sophisticated hypotheses and to develop predictive models. Decision trees are evaluated based on a library of imported datasets and can be stored in a collective area for sharing and re-use. Branch is hosted at http://biobranch.org/ and the open source code is available at http://bitbucket.org/sulab/biobranch/.

Tong Shu Li, Benjamin M. Good, Andrew I. Su

Semantic relation extraction is one of the frontiers of biomedical natural language processing research. Gold standards are key tools for advancing this research. It is challenging to generate these standards because of the high cost of expert time and the difficulty in establishing agreement between annotators. We implemented and evaluated a microtask crowdsourcing approach that can produce a gold standard for extracting drug-disease relations. The aggregated crowd judgment agreed with expert annotations from a pre-existing corpus on 43 of 60 sentences tested. The levels of crowd agreement varied in a similar manner to the levels of agreement among the original expert annotators. This work rein-forces the power of crowdsourcing in the process of assembling gold standards for relation extraction. Further, it high-lights the importance of exposing the levels of agreement between human annotators, expert or crowd, in gold standard corpora as these are reproducible signals indicating ambiguities in the data or in the annotation guidelines.

Benjamin M Good, Max Nanis, Andrew I. Su

Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language process (BioNLP) projects attempt to address this challenge, but the state of the art in BioNLP still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the training set of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was examined by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 1 week at a cost of $.06 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task such that the system can be tuned to balance cost against quality. These results demonstrate that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP.