SIA: a scalable interoperable annotation server for biomedical named entities
Abstract Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools i...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-018-0319-2 |
| _version_ | 1819092051910721536 |
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| author | Johannes Kirschnick Philippe Thomas Roland Roller Leonhard Hennig |
| author_facet | Johannes Kirschnick Philippe Thomas Roland Roller Leonhard Hennig |
| author_sort | Johannes Kirschnick |
| collection | DOAJ |
| description | Abstract Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., chemicals, diseases, genes, miRNA, mutations, and organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia. |
| first_indexed | 2024-12-21T22:49:29Z |
| format | Article |
| id | doaj.art-8b87272a24044c1985fcb98322a0aada |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-21T22:49:29Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-8b87272a24044c1985fcb98322a0aada2022-12-21T18:47:37ZengBMCJournal of Cheminformatics1758-29462018-12-011011710.1186/s13321-018-0319-2SIA: a scalable interoperable annotation server for biomedical named entitiesJohannes Kirschnick0Philippe Thomas1Roland Roller2Leonhard Hennig3DFKI Language Technology LabDFKI Language Technology LabDFKI Language Technology LabDFKI Language Technology LabAbstract Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., chemicals, diseases, genes, miRNA, mutations, and organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia.http://link.springer.com/article/10.1186/s13321-018-0319-2Text miningAnnotation serviceRobustnessScalabilityExtensibility |
| spellingShingle | Johannes Kirschnick Philippe Thomas Roland Roller Leonhard Hennig SIA: a scalable interoperable annotation server for biomedical named entities Journal of Cheminformatics Text mining Annotation service Robustness Scalability Extensibility |
| title | SIA: a scalable interoperable annotation server for biomedical named entities |
| title_full | SIA: a scalable interoperable annotation server for biomedical named entities |
| title_fullStr | SIA: a scalable interoperable annotation server for biomedical named entities |
| title_full_unstemmed | SIA: a scalable interoperable annotation server for biomedical named entities |
| title_short | SIA: a scalable interoperable annotation server for biomedical named entities |
| title_sort | sia a scalable interoperable annotation server for biomedical named entities |
| topic | Text mining Annotation service Robustness Scalability Extensibility |
| url | http://link.springer.com/article/10.1186/s13321-018-0319-2 |
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