Semantic Annotation of Experimental Methods in Analytical Chemistry

Analytical Chemistry, vol. 94, pp. 15464–15471

Abstract

A major obstacle for reusing and integrating existing data is finding the data that is most relevant in a given context. The primary metadata resource is the scientific literature describing the experiments that produced the data. To stimulate the development of natural language processing methods for extracting this information from articles, we have manually annotated 100 recent open access publications in Analytical Chemistry as semantic graphs. We focused on articles mentioning mass spectrometry in their experimental sections, as we are particularly interested in the topic, which is also within the domain of several ontologies and controlled vocabularies. The resulting gold standard dataset is publicly available and directly applicable to validating automated methods for retrieving this metadata from the literature. In the process, we also made a number of observations on the structure and description of experiments and open access publication in this journal.

Authors 9

1. Magnus Palmblad corresponding Aachen Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands

2. Enahoro Asein

   University of Tartu

   Affiliation as printed

   Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia

3. Nina P. Bergman

   Uppsala University

   Affiliation as printed

   Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden

4. A. P. Ivanova

   Uppsala University

   Affiliation as printed

   Analytical Chemistry and Neurochemistry, Department of Chemistry─BMC, Uppsala University, SE-75124 Uppsala, Sweden

5. Lukas Ramasauskas

   Uppsala University

   Affiliation as printed

   Analytical Chemistry and Neurochemistry, Department of Chemistry─BMC, Uppsala University, SE-75124 Uppsala, Sweden

6. Hazzar Mohammed Reyes

   University of Tartu

   Affiliation as printed

   Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia

7. Stefan Ruchti

   Uppsala University · University of Tartu

   Affiliation as printed

   Analytical Chemistry and Neurochemistry, Department of Chemistry─BMC, Uppsala University, SE-75124 Uppsala, Sweden

   Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia

8. Leonardo Soto-Jácome

   University of Tartu

   Affiliation as printed

   Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia

9. Jonas Bergquist

   Uppsala University

   Affiliation as printed

   Analytical Chemistry and Neurochemistry, Department of Chemistry─BMC, Uppsala University, SE-75124 Uppsala, Sweden