User:Daniel Mietchen/Semantic integration of the biodiversity literature

This page is meant to facilitate an overview of the scholarly literature pertaining to semantic integration of the biodiversity literature, along with relevant Wikipedia articles. If you are working on similar issues, please get in touch.

Recommended reading

Scholarly

• Hardisty, A.; Roberts, D.; Biodiversity Informatics Community; Addink, W.; Aelterman, B.; Agosti, D.; Amaral-Zettler, L.; Ariño, A. H.; Arvanitidis, C.; Backeljau, T.; Bailly, N.; Belbin, L.; Berendsohn; Bertrand, N.; Caithness, N.; Campbell, D.; Cochrane, G.; Conruyt, N.; Culham, A.; Damgaard, C.; Davies, N.; Fady, B.; Faulwetter; Feest, A.; Field, D.; Garnier, E.; Geser, G.; Gilbert, J. (2013). "A decadal view of biodiversity informatics: Challenges and priorities". BMC Ecology. 13: 16. doi:10.1186/1472-6785-13-16. PMID 23587026.
• Costello, M. J.; Michener, W. K.; Gahegan, M.; Zhang, Z. Q.; Bourne, P. E. (2013). "Biodiversity data should be published, cited, and peer reviewed". Trends in Ecology & Evolution. 28 (8): 454. doi:10.1016/j.tree.2013.05.002.
• Berendsohn, W.; Güntsch, A.; Hoffmann, N.; Kohlbecker, A.; Luther, K.; Müller, A. (2011). "Biodiversity information platforms: From standards to interoperability". ZooKeys. 150 (150): 71–87. doi:10.3897/zookeys.150.2166. PMC 3234432. PMID 22207807.
• King, D.; Morse, D.; Willis, A.; Dil, A. (2011). "Towards the bibliography of life". ZooKeys. 150 (150): 151–166. doi:10.3897/zookeys.150.2167. PMC 3234436. PMID 22207811.
• Penev, L.; Lyal, C.; Weitzman, A.; Morse, D.; King, D.; Sautter, G.; Georgiev, T.; Morris, R.; Catapano, T.; Agosti, D. (2011). "XML schemas and mark-up practices of taxonomic literature". ZooKeys. 150 (150): 89–116. doi:10.3897/zookeys.150.2213. PMC 3234433. PMID 22207808.
• Leon Bottou (2011). "From Machine Learning to Machine Reasoning". arXiv:1102.1808 [cs.AI].
• Miller, J.; Dikow, T.; Agosti, D.; Sautter, G.; Catapano, T.; Penev, L.; Zhang, Z. Q.; Pentcheff, D.; Pyle, R.; Blum, S.; Parr, C.; Freeland, C.; Garnett, T.; Ford, L. S.; Muller, B.; Smith, L.; Strader, G.; Georgiev, T.; Bénichou, L. (2012). "From taxonomic literature to cybertaxonomic content". BMC Biology. 10: 87. doi:10.1186/1741-7007-10-87. PMC 3485131. PMID 23114078.
• Plikus, M. V.; Zhang, Z.; Chuong, C. M. (2006). "PubFocus: Semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm". BMC Bioinformatics. 7: 424. doi:10.1186/1471-2105-7-424. PMC 1618408. PMID 17014720.
• Page, R. D. (2011). "Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library". BMC Bioinformatics. 12: 187–1522. doi:10.1186/1471-2105-12-187. PMC 3129327. PMID 21605356.
• Magurran, A. E. (2010). "Q&A: What is biodiversity?". BMC Biology. 8: 145–1356. doi:10.1186/1741-7007-8-145. PMC 3002324. PMID 21159210.
• Krell, F. T. (2012). "Electronic publication of new animal names - an interview with Frank-T. Krell, Commissioner of the International Commission on Zoological Nomenclature and Chair of the ICZN ZooBank Committee". BMC Evolutionary Biology. 12: 184–1936. doi:10.1186/1471-2148-12-184. PMC 3483210. PMID 22978411.
• Penev, L.; Agosti, D.; Georgiev, T.; Catapano, T.; Miller, J.; Blagoderov, V.; Roberts, D.; Smith, V.; Brake, I.; Ryrcroft, S.; Scott, B.; Johnson, N.; Morris, R.; Sautter, G.; Chavan, V.; Robertson, T.; Remsen, D.; Stoev, P.; Parr, C.; Knapp, S.; Kress, W. J.; Thompson, C.; Erwin, T. (2010). "Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples". ZooKeys. 50. doi:10.3897/zookeys.50.538.
• Moritz, T.; Krishnan, S.; Roberts, D.; Ingwersen, P.; Agosti, D.; Penev, L.; Cockerill, M.; Chavan, V. (2011). "Towards mainstreaming of biodiversity data publishing: Recommendations of the GBIF Data Publishing Framework Task Group". BMC Bioinformatics. 12: S1. doi:10.1186/1471-2105-12-S15-S1.
• Chavan, V.; Penev, L. (2011). "The data paper: A mechanism to incentivize data publishing in biodiversity science". BMC Bioinformatics. 12: S2. doi:10.1186/1471-2105-12-S15-S2.
• Zhou, X.; Adamowicz, S. J.; Jacobus, L. M.; Dewalt, R. E.; Hebert, P. D. (2009). "Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada". Frontiers in Zoology. 6: 30. doi:10.1186/1742-9994-6-30. PMC 2800108. PMID 20003245.
• Chavan, V. S.; Ingwersen, P. (2009). "Towards a data publishing framework for primary biodiversity data: Challenges and potentials for the biodiversity informatics community". BMC Bioinformatics. 10: S2. doi:10.1186/1471-2105-10-S14-S2.
• Hrynaszkiewicz, I.; Busch, S.; Cockerill, M. J. (2013). "Licensing the future: Report on BioMed Central's public consultation on open data in peer-reviewed journals". BMC Research Notes. 6: 318. doi:10.1186/1756-0500-6-318. PMC 3751723. PMID 23962139.
• Hrynaszkiewicz, I.; Cockerill, M. J. (2012). "Open by default: A proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals". BMC Research Notes. 5: 494. doi:10.1186/1756-0500-5-494. PMC 3465200. PMID 22958225.
• Riedel, A.; Sagata, K.; Suhardjono, Y. R.; Tänzler, R.; Balke, M. (2013). "Integrative taxonomy on the fast track - towards more sustainability in biodiversity research". Frontiers in Zoology. 10 (1): 15. doi:10.1186/1742-9994-10-15. PMID 23537182.
• Wieczorek, J.; Bloom, D.; Guralnick, R.; Blum, S.; Döring, M.; Giovanni, R.; Robertson, T.; Vieglais, D. (2012). Sarkar, Indra Neil (ed.). "Darwin Core: An Evolving Community-Developed Biodiversity Data Standard". PLoS ONE. 7 (1): e29715. doi:10.1371/journal.pone.0029715. PMC 3253084. PMID 22238640.
• Zhang, Z.; Cheung, K. -H.; Townsend, J. P. (2008). "Bringing Web 2.0 to bioinformatics". Briefings in Bioinformatics. 10 (1): 1–10. doi:10.1093/bib/bbn041. PMC 2638627. PMID 18842678.
  • seen in this comment
• Balke, M.; Schmidt, S.; Hausmann, A.; Toussaint, E. F.; Bergsten, J.; Buffington, M.; Häuser, C. L.; Kroupa, A.; Hagedorn, G.; Riedel, A.; Polaszek, A.; Ubaidillah, R.; Krogmann, L.; Zwick, A.; Fiká Ek, M.; Hájek, J. Í.; Michat, M. C.; Dietrich, C.; La Salle, J.; Mantle, B.; Ng, P. K.; Hobern, D. (2013). "Biodiversity into your hands - A call for a virtual global natural history 'metacollection'". Frontiers in Zoology. 10 (1): 55. doi:10.1186/1742-9994-10-55. PMID 24044698.
• Sansone, S. A.; Rocca-Serra, P.; Field, D.; Maguire, E.; Taylor, C.; Hofmann, O.; Fang, H.; Neumann, S.; Tong, W.; Amaral-Zettler, L.; Begley, K.; Booth, T.; Bougueleret, L.; Burns, G.; Chapman, B.; Clark, T.; Coleman, L. A.; Copeland, J.; Das, S.; De Daruvar, A.; De Matos, P.; Dix, I.; Edmunds, S.; Evelo, C. T.; Forster, M. J.; Gaudet, P.; Gilbert, J.; Goble, C.; Griffin, J. L.; Jacob, D. (2012). "Toward interoperable bioscience data". Nature Genetics. 44 (2): 121–126. doi:10.1038/ng.1054. PMC 3428019. PMID 22281772.
• Yamamoto, Y.; Yamaguchi, A.; Yonezawa, A. (2013). "Building Linked Open Data towards integration of biomedical scientific literature with DBpedia". Journal of Biomedical Semantics. 4 (1): 8. doi:10.1186/2041-1480-4-8. PMC 3621846. PMID 23497538.
• Altschul, S.; Demchak, B.; Durbin, R.; Gentleman, R.; Krzywinski, M.; Li, H.; Nekrutenko, A.; Robinson, J.; Rasband, W.; Taylor, J.; Trapnell, C. (2013). "The anatomy of successful computational biology software". Nature Biotechnology. 31 (10): 894–897. doi:10.1038/nbt.2721. PMID 24104757.
• Budura, A.; Cudré-Mauroux, P.; Aberer, K. (2007). "From bioinformatic web portals to semantically integrated Data Grid networks". Future Generation Computer Systems. 23 (3): 485. doi:10.1016/j.future.2006.03.002.
• Beck, J. (2011). "NISO Z39.96 the Journal Article Tag Suite (JATS): What Happened to the NLM DTDs?". The Journal of Electronic Publishing. 14. doi:10.3998/3336451.0014.106.
• Needleman, M. H. (2012). "NISO Z39.96-201x, JATS: Journal Article Tag Suite". Serials Review. 38 (3): 213–214. doi:10.1016/j.serrev.2012.08.006.
• Preserving and Publishing Digital Content Using XML Workflows. In A.P. Brown (Ed.), The Library Publishing Toolkit (pp. 97-108). Geneseo, NY: IDS Project Press. http://hdl.handle.net/2027.42/99563
• Page, R. (2009). "BioGUID: Resolving, discovering, and minting identifiers for biodiversity informatics". BMC Bioinformatics. 10: S5. doi:10.1186/1471-2105-10-S14-S5. PMC 2775151. PMID 19900301.
• Bourne, P. (2005). "Will a Biological Database Be Different from a Biological Journal?". PLoS Computational Biology. 1 (3): e34. doi:10.1371/journal.pcbi.0010034. PMC 1193993. PMID 16158097.
• Agosti, D.; Egloff, W. (2009). "Taxonomic information exchange and copyright: The Plazi approach". BMC Research Notes. 2: 53. doi:10.1186/1756-0500-2-53. PMC 2673227. PMID 19331688.
• Fontaine, B. T.; Van Achterberg, K.; Alonso-Zarazaga, M. A.; Araujo, R.; Asche, M.; Aspöck, H.; Aspöck, U.; Audisio, P.; Aukema, B.; Bailly, N.; Balsamo, M.; Bank, R. A.; Belfiore, C.; Bogdanowicz, W.; Boxshall, G.; Burckhardt, D.; Chylarecki, P. A.; Deharveng, L.; Dubois, A.; Enghoff, H.; Fochetti, R.; Fontaine, C.; Gargominy, O.; Gomez Lopez, M. S. G.; Goujet, D.; Harvey, M. S.; Heller, K. G.; Van Helsdingen, P.; Hoch, H.; De Jong, Y. (2012). Schierwater, Bernd (ed.). "New Species in the Old World: Europe as a Frontier in Biodiversity Exploration, a Test Bed for 21st Century Taxonomy". PLoS ONE. 7 (5): e36881. doi:10.1371/journal.pone.0036881. PMC 3359328. PMID 22649502.
• Lasko, T. A.; Hauser, S. E. (2000). "Approximate string matching algorithms for limited-vocabulary OCR output correction". In Kantor, Paul B; Lopresti, Daniel P; Zhou, Jiangying (eds.). Document Recognition and Retrieval VIII. Document Recognition and Retrieval VIII. 4307. p. 232. doi:10.1117/12.410841.
• Maddison, D. R.; Guralnick, R.; Hill, A.; Reysenbach, A. L.; McDade, L. A. (2012). "Ramping up biodiversity discovery via online quantum contributions". Trends in Ecology & Evolution. 27 (2): 72. doi:10.1016/j.tree.2011.10.010.
• Coles, S. J.; Frey, J. G.; Bird, C. L.; Whitby, R. J.; Day, A. E. (2013). "First steps towards semantic descriptions of electronic laboratory notebook records". Journal of Cheminformatics. 5: 52. doi:10.1186/1758-2946-5-52.
• Frey, J. G.; Bird, C. L. (2013). "Cheminformatics and the Semantic Web: Adding value with linked data and enhanced provenance". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (5): 465. doi:10.1002/wcms.1127.
• Masum, H.; Rao, A.; Good, B. M.; Todd, M. H.; Edwards, A. M.; Chan, L.; Bunin, B. A.; Su, A. I.; Thomas, Z.; Bourne, P. E. (2013). "Ten Simple Rules for Cultivating Open Science and Collaborative R&D". PLoS Computational Biology. 9 (9): e1003244. doi:10.1371/journal.pcbi.1003244.
• Hrynaszkiewicz, I.; Busch, S.; Cockerill, M. J. (2013). "Licensing the future: Report on BioMed Central's public consultation on open data in peer-reviewed journals". BMC Research Notes. 6: 318. doi:10.1186/1756-0500-6-318. PMC 3751723. PMID 23962139.
• MacLean, D. (2013). "Changing the rules of the game". ELife. 2: e01294. doi:10.7554/eLife.01294.
• Desjardins-Proulx, P.; White, E. P.; Adamson, J. J.; Ram, K.; Poisot, T. E.; Gravel, D. (2013). "The Case for Open Preprints in Biology". PLoS Biology. 11 (5): e1001563. doi:10.1371/journal.pbio.1001563.
• Strong, M.; Shee, K.; Guido, N. J.; Lue, R. A.; Church, G. M.; Viel, A. (2010). "Research, Collaboration, and Open Science Using Web 2.0". Journal of Microbiology & Biology Education. 11 (2). doi:10.1128/jmbe.v11i2.219.
• Breeze, J. L.; Poline, J. B.; Kennedy, D. N. (2012). "Data sharing and publishing in the field of neuroimaging". GigaScience. 1: 9. doi:10.1186/2047-217X-1-9.
• Marshall, J. (2013). "Kickstart your research". Proceedings of the National Academy of Sciences. 110 (13): 4857. doi:10.1073/pnas.1303517110.
• Gorgolewski, K. J.; Margulies, D. S.; Milham, M. P. (2013). "Making Data Sharing Count: A Publication-Based Solution". Frontiers in Neuroscience. 7. doi:10.3389/fnins.2013.00009.
• Kriegeskorte, N.; Walther, A.; Deca, D. (2012). "An emerging consensus for open evaluation: 18 visions for the future of scientific publishing". Frontiers in Computational Neuroscience. 6. doi:10.3389/fncom.2012.00094.
• Thessen, A.; Patterson, D. (2011). "Data issues in the life sciences". ZooKeys. 150: 15. doi:10.3897/zookeys.150.1766.
• Molloy, J. C. (2011). "The Open Knowledge Foundation: Open Data Means Better Science". PLoS Biology. 9 (12): e1001195. doi:10.1371/journal.pbio.1001195. PMC 3232214. PMID 22162946.
• Murray-Rust, P. (2011). "Semantic science and its communication - a personal view". Journal of Cheminformatics. 3: 48–11. doi:10.1186/1758-2946-3-48. PMC 3206456. PMID 21999715.

Information extraction and Natural language processing

“ All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge. ” — Grimaldi & Engel, 2005, Evolution of the Insects

JATS-Con papers

Overview.

• Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher
• Reducing costs and expanding XML submissions with PDF to JATS conversion
• Inconsistent XML as a Barrier to Reuse of Open Access Content
• Book Publishing with JATS
• From Markup to Linked Data: Mapping NISO JATS v1.0 to RDF using the SPAR (Semantic Publishing and Referencing) Ontologies

Wikipedia

• Biodiversity
• Annotation
• Markup language
• Semantic Web
• Linked Open Data (LOD)
• Biodiversity Heritage Library (BHL)
• Biodiversity Heritage Library for Europe (BHL-Europe)
• Web Ontology Language (OWL)
• Biodiversity Information Standards (TDWG)
• Expert system
• Astronomical naming conventions
  • cited on Taxacom as an example for naming and classification systems working independently
• Optical character recognition
• Serialization