Structured digital tables on the Semantic Web: toward a structured digital literature
In parallel to the growth in bioscience databases, biomedical publications have increased exponentially in the past decade. However, the extraction of high‐quality information from the corpus of scientific literature has been hampered by the lack of machine‐interpretable content, despite text‐mining...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2010-01-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2010.45 |
| _version_ | 1797281853427679232 |
|---|---|
| author | Kei‐Hoi Cheung Matthias Samwald Raymond K Auerbach Mark B Gerstein |
| author_facet | Kei‐Hoi Cheung Matthias Samwald Raymond K Auerbach Mark B Gerstein |
| author_sort | Kei‐Hoi Cheung |
| collection | DOAJ |
| description | In parallel to the growth in bioscience databases, biomedical publications have increased exponentially in the past decade. However, the extraction of high‐quality information from the corpus of scientific literature has been hampered by the lack of machine‐interpretable content, despite text‐mining advances. To address this, we propose creating a structured digital table as part of an overall effort in developing machine‐readable, structured digital literature. In particular, we envision transforming publication tables into standardized triples using Semantic Web approaches. We identify three canonical types of tables (conveying information about properties, networks, and concept hierarchies) and show how more complex tables can be built from these basic types. We envision that authors would create tables initially using the structured triples for canonical types and then have them visually rendered for publication, and we present examples for converting representative tables into triples. Finally, we discuss how ‘stub’ versions of structured digital tables could be a useful bridge for connecting together the literature with databases, allowing the former to more precisely document the later. |
| first_indexed | 2024-03-07T17:03:26Z |
| format | Article |
| id | doaj.art-fd0c0b89925f470185833b162050e934 |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-03-07T17:03:26Z |
| publishDate | 2010-01-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-fd0c0b89925f470185833b162050e9342024-03-03T03:11:51ZengSpringer NatureMolecular Systems Biology1744-42922010-01-0161n/an/a10.1038/msb.2010.45Structured digital tables on the Semantic Web: toward a structured digital literatureKei‐Hoi Cheung0Matthias Samwald1Raymond K Auerbach2Mark B Gerstein3Program in Computational Biology and Bioinformatics, Yale University New Haven CT USADigital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park Lower Dangan Galway IrelandProgram in Computational Biology and Bioinformatics, Yale University New Haven CT USAProgram in Computational Biology and Bioinformatics, Yale University New Haven CT USAIn parallel to the growth in bioscience databases, biomedical publications have increased exponentially in the past decade. However, the extraction of high‐quality information from the corpus of scientific literature has been hampered by the lack of machine‐interpretable content, despite text‐mining advances. To address this, we propose creating a structured digital table as part of an overall effort in developing machine‐readable, structured digital literature. In particular, we envision transforming publication tables into standardized triples using Semantic Web approaches. We identify three canonical types of tables (conveying information about properties, networks, and concept hierarchies) and show how more complex tables can be built from these basic types. We envision that authors would create tables initially using the structured triples for canonical types and then have them visually rendered for publication, and we present examples for converting representative tables into triples. Finally, we discuss how ‘stub’ versions of structured digital tables could be a useful bridge for connecting together the literature with databases, allowing the former to more precisely document the later.https://doi.org/10.1038/msb.2010.45bioinformaticsdata integrationsemantic publishingSemantic Webtriplification |
| spellingShingle | Kei‐Hoi Cheung Matthias Samwald Raymond K Auerbach Mark B Gerstein Structured digital tables on the Semantic Web: toward a structured digital literature Molecular Systems Biology bioinformatics data integration semantic publishing Semantic Web triplification |
| title | Structured digital tables on the Semantic Web: toward a structured digital literature |
| title_full | Structured digital tables on the Semantic Web: toward a structured digital literature |
| title_fullStr | Structured digital tables on the Semantic Web: toward a structured digital literature |
| title_full_unstemmed | Structured digital tables on the Semantic Web: toward a structured digital literature |
| title_short | Structured digital tables on the Semantic Web: toward a structured digital literature |
| title_sort | structured digital tables on the semantic web toward a structured digital literature |
| topic | bioinformatics data integration semantic publishing Semantic Web triplification |
| url | https://doi.org/10.1038/msb.2010.45 |
| work_keys_str_mv | AT keihoicheung structureddigitaltablesonthesemanticwebtowardastructureddigitalliterature AT matthiassamwald structureddigitaltablesonthesemanticwebtowardastructureddigitalliterature AT raymondkauerbach structureddigitaltablesonthesemanticwebtowardastructureddigitalliterature AT markbgerstein structureddigitaltablesonthesemanticwebtowardastructureddigitalliterature |