Abstract
We present an automatic workflow that performs text segmentation and entity extraction from scientific literature to primarily address Task 2 of the Semantic Publishing Challenge 2015. The goal of Task 2 is to extract various information from full-text papers to represent the context in which a document is written, such as the affiliation of its authors and the corresponding funding bodies. Our proposed solution is composed of two subsystems: (i) A text mining pipeline, developed based on the GATE framework, which extracts structural and semantic entities, such as authors’ information and references, and produces semantic (typed) annotations; and (ii) a flexible exporting module, the LODeXporter, which translates the document annotations into RDF triples according to custom mapping rules. Additionally, we leverage existing Named Entity Recognition (NER) tools to extract named entities from text and ground them to their corresponding resources on the Linked Open Data cloud, thus, briefly covering Task 3 objectives, which involves linking of detected entities to resources in existing open datasets. The output of our system is an RDF graph stored in a scalable TDB-based storage with a public SPARQL endpoint for the task’s queries.
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Notes
- 1.
Semantic Publishing Challenge 2015, https://github.com/ceurws/lod/wiki/SemPub2015.
- 2.
Tokens are smallest, meaningful units of text, such as words, numbers or symbols.
- 3.
Argumentation Zoning (AZ) Corpus, http://www.cl.cam.ac.uk/~sht25/AZ_corpus.html.
- 4.
The root or lemma of a word is its canonical form without any inflectional endings.
- 5.
Task 2 Dataset, https://github.com/ceurws/lod/wiki/Task2#data-source.
- 6.
Resource Description Framework (RDF), http://www.w3.org/RDF/.
- 7.
Best Practices for Publishing Linked Data, http://www.w3.org/TR/ld-bp/.
- 8.
Discourse Elements Ontology (DEO), http://purl.org/spar/deo.
- 9.
PUBlication Ontology, http://lod.semanticsoftware.info/pubo/pubo.rdf.
- 10.
Document Components Ontology (DoCO), http://purl.org/spar/doco.
- 11.
Originally called the “RDF Mapper”, it is now an independent open source project available at http://www.semanticsoftware.info/lodexporter.
- 12.
Xpdf, http://www.foolabs.com/xpdf/.
- 13.
Several of our named entity extraction rules are extensions of GATE’s ANNIE plugin [5].
- 14.
Apache Jena, http://jena.apache.org.
- 15.
Apache TDB, http://jena.apache.org/documentation/tdb/.
- 16.
Precision is the fraction of extracted annotations that are relevant.
- 17.
Recall is the fraction of relevant annotations that are extracted.
- 18.
F-measure is the harmonic mean between Precision and Recall.
- 19.
The zero recall for our Q2.5 was due to an error in the mapping rules, where an entity was mapped to two different classes. Apart from that, the annotations were correctly extracted.
References
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Sateli, B., Witte, R. (2015). Automatic Construction of a Semantic Knowledge Base from CEUR Workshop Proceedings. In: Gandon, F., Cabrio, E., Stankovic, M., Zimmermann, A. (eds) Semantic Web Evaluation Challenges. SemWebEval 2015. Communications in Computer and Information Science, vol 548. Springer, Cham. https://doi.org/10.1007/978-3-319-25518-7_11
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