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Interoperability of corpus processing work-flow engines: the case of AlvisNLP/ML in OpenMinTeD

Authors: Ba, Mouhamadou; Bossy, Robert;

Interoperability of corpus processing work-flow engines: the case of AlvisNLP/ML in OpenMinTeD

Abstract

AlvisNLP/ML is a corpus processing engine developed by the Bibliome group. It has been used in several experiments and end-user applications. We describe its design principles and data and workflow models, then we discuss interoperability challenges in the context of the OpenMinTeD project. The objective of OpenMinTeD (EC/H2020) is to create an infrastructure for Text and Data Mining (TDM) of scientific and scholarly publications. In order to offer to the infrastructure users a single entry point and the widest range of tools as possible, the major European corpus processing engines will be made interoperable, including Argo, DKPro, and GATE. We show that AlvisNLP/ML can be fully integrated into the OpenMinTeD platform while maintaining its originality.

Country
France
Keywords

platform, corpus processing, Workflow, Interoperability, OpenMinTeD, Processing Workflows, [SDV]Life Sciences [q-bio], Text-mining;platform;interoperability;Natural Language Processing;Workflow;Processing Workflows;Software Interoperability, Software Interoperability, interoperability, Text-mining, Natural Language Processing, Workflow

20 references, page 1 of 2

Bossy, R., Kotoujansky, A., Aubin, S., and Nedellec, C. (2008). Close integration of ML and NLP tools in BioAlvis for semantic search in bacteriology. Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, UK. [OpenAIRE]

Bossy, R., Jourde, J., Manine, A., Veber, P., Alphonse, E´., van de Guchte, M., Bessie`res, P., and Nedellec, C. (2012). Bionlp shared task - the bacteria track. BMC Bioinformatics, 13(S-11):S3. [OpenAIRE]

Bossy, R., Golik, W., Ratkovic, Z., Valsamou, D., Bessie`res, P., and Ne´dellec, C. (2015). Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task. BMC Bioinformatics, 16(10):1- 16.

Comeau, D. C., Islamaj Dogan, R., Ciccarese, P., Cohen, K. B., Krallinger, M., Leitner, F., Lu, Z., Peng, Y., Rinaldi, F., Torii, M., Valencia, A., Verspoor, K., Wiegers, T. C., Wu, C. H., and Wilbur, W. J. (2013). BioC: a minimalist approach to interoperability for biomedical text processing. Database, 2013. [OpenAIRE]

Cunningham, H., Tablan, V., Roberts, A., and Bontcheva, K. (2013). Getting more out of biomedical documents with GATE's full lifecycle open source text analytics. PLoS Comput Biol, 9:1-16, 02.

Day-Richter, J., Harris, M. A., Haendel, M., Gene Ontology OBO-Edit Working Group, and Lewis, S. (2007). OBO-Edit-an ontology editor for biologists. Bioinformatics (Oxford, England), 23(16):2198-2200, August.

Eckart de Castilho, R. and Gurevych, I. (2014). A broadcoverage collection of portable NLP components for building shareable analysis pipelines. In Proceedings of the Workshop on Open Infrastructures and Analysis Frameworks for HLT, pages 1-11, Dublin, Ireland, August. Association for Computational Linguistics and Dublin City University.

Ferrucci, D. and Lally, A. (2004). UIMA: An architectural approach to unstructured information processing in the corporate research environment. Nat. Lang. Eng., 10(3- 4):327-348.

Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005). Galaxy: a platform for interactive large-scale genome analysis. Genome research, 15(10):1451-1455. [OpenAIRE]

Golik, W., Dameron, O., Bugeon, J., Fatet, A., Hue, I., Hurtaud, C., Reichstadt, M., Salau¨ n, M.-C., Vernet, J., Joret, L., et al. (2012). ATOL: the multi-species livestock trait ontology. In Metadata and Semantics Research, pages 289-300. Springer Berlin Heidelberg. [OpenAIRE]

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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    4
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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download
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
downloads
OpenAIRE UsageCountsDownloads provided by UsageCounts
4
Average
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58
26
Green
Funded by
EC| OpenMinTeD
Project
OpenMinTeD
Open Mining INfrastructure for TExt and Data
  • Funder: European Commission (EC)
  • Project Code: 654021
  • Funding stream: H2020 | RIA
Validated by funder
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