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.; et al. (2013). "A decadal view of biodiversity informatics: Challenges and priorities". BMC Ecology. 13: 16. doi:10.1186/1472-6785-13-16. PMC 3843378. PMID 23587026.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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): 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): 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): 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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): 1–16. doi:10.3897/zookeys.50.538. PMC 3088020. PMID 21594113.
• 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. PMC 3287444. PMID 22373150.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMID 22373175. S2CID 5405280.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMC 2775148. PMID 19900298.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMC 3626550. PMID 23537182.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMC 3848749. PMID 24044698.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMC 4166496. 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 (1). doi:10.3998/3336451.0014.106. PMC 3227009. PMID 22140303.
• 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. S2CID 62679460.
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• Bourne, P. (2005). "Will a Biological Database Be Different from a Biological Journal?". PLOS Computational Biology. 1 (3): 179–181. doi:10.1371/journal.pcbi.0010034. PMC 1193993. PMID 16158097.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. Vol. 4307. pp. 232–240. doi:10.1117/12.410841. S2CID 8471146.
• 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): 72–77. doi:10.1016/j.tree.2011.10.010. PMID 22118809.
• 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. S2CID 15257750.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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): 465–481. doi:10.1002/wcms.1127. PMC 3884755. PMID 24432050.
• 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. PMC 3784487. PMID 24086123.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• MacLean, D. (2013). "Changing the rules of the game". eLife. 2: e01294. doi:10.7554/eLife.01294. PMC 3743132. PMID 23951548.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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. PMC 3653830. PMID 23690752.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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): 130–134. doi:10.1128/jmbe.v11i2.219. PMC 3577171. PMID 23653712.
• Breeze, J. L.; Poline, J. B.; Kennedy, D. N. (2012). "Data sharing and publishing in the field of neuroimaging". GigaScience. 1 (1): 9. doi:10.1186/2047-217X-1-9. PMC 3626511. PMID 23587272.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• Marshall, J. (2013). "Kickstart your research". Proceedings of the National Academy of Sciences. 110 (13): 4857–4859. 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): 15–51. doi:10.3897/zookeys.150.1766. PMC 3234430. PMID 22207805.
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)

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