Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
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San Joaquin River Up-Stream DO TMDL Project Task 4: Monitoring Study Interim Task Report #3

The purpose of the Dissolved Oxygen Total Maximum Daily Load Project (DO TMDLProject) is to provide a comprehensive understanding of the sources and fate of oxygen consuming materials in the San Joaquin River (SJR) watershed between Channel Point and Lander Avenue (upstream SJR). When completed, this study will provide the stakeholders an understanding of the baseline conditions of the basin, provide input for an allocation decision, and provide the stakeholders with a tool for measuring the impact of any waterquality management program that may be implemented as part of the DO TMDL process. Previous studies have identified algal biomass as the most significant oxygen-demanding substance in the DO TMDL Project study-area between of Channel Point and Lander Ave onthe SJR. Other oxygen-demanding substances found in the upstream SJR include ammonia and organic carbon from sources other than algae. The DO TMDL Project study-area contains municipalities, dairies, wetlands, cattle ranching, irrigated agriculture, and industries that could potentially contribute biochemical oxygen demand (BOD) to the SJR. This study is designed to discriminate between algal BOD and other sources of BOD throughout the entire upstream SJR watershed. Algal biomass is not a conserved substance, but grows and decays in the SJR; hence, characterization of oxygen-demanding substances in the SJR is inherently complicated and requires an integrated effort of extensive monitoring, scientific study, and modeling. In order to achieve project objectives, project activities were divided into a number of Tasks with specific goals and objectives. In this report, we present the results of monitoring and research conducted under Task 4 of the DO TMDL Project. The major objective of Task 4 is to collect sufficient hydrologic (flow) and water quality (WQ) data to characterize the loading of algae, other oxygen-demanding materials, and nutrients from individual tributaries and sub-watersheds of the upstream SJR between Mossdale and Lander Avenue. This data is specifically being collected to provide data for the Task 6 Modeling effort. Task 4 provides input and calibration data for flow and WQ modeling associated with the low DO problems in the SJR watershed, including modeling on the linkage among nutrients, algae, and low DO. Task 4 is providing a higher volume of high quality and coherent data to the modeling team than was available in the past for the upstream SJR. The monitoring and research activities under Task 4 are integrated with the Modeling effort (Task 6) and are not designed to be a stand alone program. Although, the majority of analysis of the Task 4 data is occurring as part of the Task 6 Modeling program, analysis of Task 4 data independently of the modeling effort is also an important component of the DO TMDL Project effort. In this report, we present the results of monitoring and research conducted under Task 4. The major purposes of this report are to 1) document activities undertaken as part of the DOTMDL Project; 2) organize electronic data for delivery to State agencies, stakeholders and principal investigators (cooperators) on the DO TMDL Project; 3) provide a summary analysis of the data for reference and to assist stakeholders in planning watershed activities inresponse to the DO TMDL requirements; and 5) provide a preliminary scientific interpretation independently of the Task 6 Modeling effort. Due to the extensive scope of theTask 4 portion of the DO TMDL Project, the Task 4 March 2007 Interim Report is divided into a numbers of chapters and associated appendixes designed to be able to stand1-3 independently of each other. The purpose of this chapter is to provide an overview of Task 4 data collection and to explain the structure of the overall report