XML schemas and mark-up practices of taxonomic literature

ZooKeys

Volumn 150, Issue , 2011, Pages 89-116

  Penev, Lyubomir ^a   Lyal, Christopher H C ^b   Weitzman, Anna ^c   Morse, David R ^d   King, David ^d   Sautter, Guido ^e   Georgiev, Teodor ^f   Morris, Robert A ^g   Catapano, Terry ^h   Agosti, Donat ^h  

^a BULGARIAN ACADEMY OF SCIENCES   (Bulgaria)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c SMITHSONIAN INSTITUTION   (United States)

^d OPEN UNIVERSITY   (United Kingdom)

^e KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^f Pensoft Publishers   (Bulgaria)

^g UNIVERSITY OF MASSACHUSETTS BOSTON   (United States)

^h Plazi   (Switzerland)

Author keywords

Mark up; TaXMLit; Taxonomy; TaxonX; TaxPub; XML schema

Indexed keywords

EID: 84856442014     PISSN: 13132989     EISSN: 13132970     Source Type: Journal    
DOI: 10.3897/zookeys.150.2213     Document Type: Review

References (35)

1. ABCD - Access to Biological Collection Data - A joint CODATA and TDWG initiative. http://www.bgbm.org/TDWG/CODATA/
2. Agosti D, Egloff W (2009) Taxonomic information exchange and copyright: the Plazi approach. BMC Research Notes 2: 53. http://www.biomedcentral.com/1756-0500/2/53 doi: 10.1186/1756-0500-2-53
3. Agosti D, Klingenberg C, Sautter G, Johnson N, Stephenson C, Catapano T (2007) Why not let the computer save you time by reading the taxonomic papers for you? Biológico, São Paulo 69 (suplemento 2): 545-548. http://hdl.handle.net/10199/15441
4. Blagoderov V, Brake I, Georgiev T, Penev L, Roberts D, Rycroft S, Scott B, Agosti D, Catapano T, Smith VS (2010a) Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys. ZooKeys 50: 17-28. doi: 10.3897/zookeys.50.539
5. Blagoderov V, Hippa H, Nel A (2010b) Parisognoriste, a new genus of Lygistorrhinidae (Diptera, Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier. ZooKeys 50: 79-90. doi: 10.3897/zookeys.50.506
6. Brake I, von Tschirnhaus M (2010) Stomosis arachnophila sp. n., a new kleptoparasitic species of freeloader flies (Diptera, Milichiidae). ZooKeys 50: 91-96. doi: 10.3897/zookeys.50.505
7. Catapano T (2010) TaxPub: An extension of the NLM/NCBI Journal Publishing DTD for taxonomic descriptions. Proceedings of the Journal Article Tag Suite Conference 2010. http://www.ncbi.nlm.nih.gov/books/NBK47081/#ref2
8. Catapano T, Weitzman AL (2007) Progress in making literature easily accessible: schemas and marking up TaxonX / Goldengate & taXMLit / INOTAXA. TDWG Annual Meeting 2007. http://wiki.tdwg.org/twiki/pub/Literature/WebHome/Catapano_Weitzman_Markup_Final.pdf
9. Cui H (2008a) Converting Taxonomic Descriptions To New Digital Formats. Biodiversity Informatics 5: 20-40. https://journals.ku.edu/index.php/jbi/article/view/46/1551
10. Cui H (2008b) Approaches to Semantic Mark-up for Natural Heritage Literature. Proceedings of the iConference 2008. http://ischools.org/conference08/pc/PA5-2_iconf08.doc
11. Cui H, Heidorn PB (2007) The reusability of induced knowledge for the automatic semantic mark-up of taxonomic descriptions. Journal of the American Society for Information Science and Technology. 58(1): 133-149. http://www3.interscience.wiley.com/cgi-bin/fulltext/113466052/PDFSTART doi: 10.1002/asi.20463
12. Cui H, Jiang Y, Sanyal PP (2010a) From Text to RDF Triple Store: An Application for Biodiversity Literature[Demo]. Proceedings of the 73rd ASIS&T Annual Meeting v. 47. Oct 22-27, 2010. Pittsburg, PA. http://www.asis.org/asist2010/proceedings/proceedings/ASIST_AM10/submissions/415_Final_Submission.pdf
13. Cui H, Boufford D, Selden P (2010b) Semantic Annotation of Biosystematics Literature without Training Examples. Journal of American Society of Information Science and Technology. 61 (3): 522-542. http://harvard.academia.edu/DavidBoufford/Papers/740926/Semantic_annotation_of_biosystematics_literature_without_training_examples
14. Curry GB, Connor, RJ (2007) Automated extraction of biodiversity data from taxonomic descriptions. In: Curry GB, Humphries CJ (Eds) Biodiversity databases: Techniques, politics, and applications: Systematics Association Special Volume 73: Boca Raton, Florida, CRC Press, Chapter 6: 63-81.
15. Curry GB, Connor RCH (2008) Automated extraction of data from text using an XML parser: An earth science example using fossil descriptions. Geosphere 4(1): 159-169. doi: 10.1130/GES00140.1
16. Darwin Core (2008) http://rs.tdwg.org/dwc/
17. Hagedorn G, Thiele K, Morris R, Heidorn PB (2005) The Structured Descriptive Data (SDD) w3c-xml-schema, version 1.0. http://www.tdwg.org/standards/116/
18. Heidorn PB, Cui H, Yu B, Wu J, Zhang H (2002) Taxonomic description creation, search and display in XML. Abstract. Botany 2002. http://www.isrl.illinois.edu/~pheidorn/papers/Botany2002Abstract.pdf
19. Kirkup D, Malcolm P, Christian G, Paton A (2005) Towards a digital African Flora. Taxon 5(2): 457-466. doi: 10.2307/25065373
20. Lyal CHC, Weitzman L (2008) Releasing the content of taxonomic papers: solutions to access and data mining. Proceedings of the BNCOD Workshop "Biodiversity Informatics: challenges in modelling and managing biodiversity knowledge" http://biodiversity.cs.cf.ac.uk/bncod/LyalAndWeitzman.pdf
21. Morse D, Dil A, King D, Willis A, Roberts D, Lyal C (2009) Improving search in scanned documents: Looking for OCR mismatches. In: Bernardi R, Chambers S, Gottfried B (Eds) Proceedings of the workshop on advanced technologies for digital libraries (AT- 4DL 2009): 58-61 http://www.unibz.it/en/public/universitypress/publications/all/Documents/9788860460301.pdf
22. Murray-Rust P, Rzepa HS (2002) Scientific publications in XML - towards a global knowledge base. Data Science 1: 84-98. doi: 10.2481/dsj.1.84
23. Parr CS, Lyal CHC (2007) Use cases for online taxonomic literature from taxonomists, conservationists, and others. TDWG Annual Conference, Slovakia http://www.tdwg.org/proceedings/article/view/269.
24. 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, Thompson C, Erwin T (2010a) Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. ZooKeys 50: 1-16. doi: 10.3897/zookeys.50.538
25. Penev L, Roberts D, Smith V, Agosti D, Erwin T (2010b) Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research. ZooKeys 50: 1-4. doi: 10.3897/zookeys.50.543
26. Penev L, Hagedorn G, Mietchen D, Georgiev T, Stoev P, Sautter G, Agosti D, Plank A, Balke M, Hendrich L, Erwin T (2011) Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID. ZooKeys 90: 1-12. doi: 10.3897/zookeys.90.1369
27. Pyle RL, Earle JL, Greene BD (2008) Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacentridae) from deep coral reefs in the tropical western Pacific. Zootaxa 1671:3-31.
28. Sautter G, Böhm K, Agosti D (2007a) A Quantitative Comparison of XML Schemas for Taxonomic Publications. Biodiversity Informatics 4: 1-13. https://journals.ku.edu/index.php/jbi/article/view/36
29. Sautter G, Agosti D, Böhm K (2007b) Semi-Automated XML Markup of Biosystematics Legacy Literature with the GoldenGATE Editor. Proceedings of PSB 2007, Wailea, HI, USA, 2007. http://psb.stanford.edu/psb-online/proceedings/psb07/sautter.pdf
30. Stoev P, Akkari N, Zapparoli M, Porco D, Enghoff H, Edgecombe GD, Georgiev T, Penev L (2010) The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group. ZooKeys 50: 29-77. doi: 10.3897/zookeys.50.504
31. Taekul C, Johnson NF, Masner L, Polaszek A, Rajmohana K. (2010) World species of the genus Platyscelio Kieffer (Hymenoptera, Platygastridae). ZooKeys 50: 97-126. doi: 10.3897/zookeys.50.485
32. TDWG (2007 onwards) TDWG: standards. Biodiversity Information Standards. http://www.tdwg.org/standards/
33. Weitzman AL, Lyal CHC (2004) An XML schema for taxonomic literature - taXMLit - http://www.sil.si.edu/digitalcollections/bca/documentation/taXMLitv1-3Intro.pdf
34. Weitzman AL, Lyal CHC (2006) INOTAXA - INtegrated Open TAXonomic Access and the "Biologia Centrali-Americana". Proceedings Of The Contributed Papers Sessions Biomedical And Life Sciences Division, SLA. 8pp. http://units.sla.org/division/dbio/Baltimore/index.html
35. Willis A, King D, Morse D, Dil A, Lyal C, Roberts D (2010) From XML to XML: The Why and How of Making the Biodiversity Literature Accessible to Researchers. Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC'10). Valletta, Malta: European Language Resources Association (ELRA). http://www.lrec-conf.org/proceedings/lrec2010/pdf/787_Paper.pdf