TY - JOUR T1 - Episodic radiations in the fly tree of life JF - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2011 DO - 10.1073/pnas.1012675108 A1 - Brian M. Wiegmann A1 - Michelle D. Trautwein A1 - Isaac S. Winkler A1 - Norman B. Barr A1 - Jung-Wook Kim A1 - Christine Lambkin A1 - Matthew A. Bertone A1 - Brian K. Cassel A1 - Keith M. Bayless A1 - Alysha M. Heimberg A1 - Benjamin M. Wheeler A1 - Kevin J. Peterson A1 - Pape, Thomas A1 - Sinclair, Bradley J. A1 - Jeffrey H. Skevington A1 - Vladimir A. Blagoderov A1 - Jason Caravas A1 - Sujatha Narayanan Kutty A1 - Urs Schmidt-Ott A1 - Gail E. Kampmeier A1 - Thompson, F. Christian A1 - Grimaldi, David A. A1 - Andrew T. Beckenbach A1 - Gregory W. Courtney A1 - Markus Friedrich A1 - Rudolf Meier A1 - Yeates, David K. L2 - 45413 L3 - 46414 ER - TY - JOUR T1 - Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples JF - ZooKeys Y1 - 2010 DO - 10.3897/zookeys.50.538 A1 - Penev, Lyubomir A1 - Agosti, Donat A1 - Georgiev, Teodor A1 - Catapano, Terrence A1 - Miller, Jeremy A1 - Vladimir A. Blagoderov A1 - Roberts, David A1 - Smith, Vincent A1 - Brake, Irina A1 - Rycroft, Simon A1 - Scott, Ben A1 - Johnson, Norman F. A1 - Morris, Robert A. A1 - Sautter, Guido A1 - Chavan, Vishwas A1 - Robertson, Tim A1 - Remsen, David A1 - Stoev, Pavel A1 - Parr, Cynthia A1 - Knapp, Sandra A1 - Kress, W. John A1 - Thompson, F. Christian A1 - Erwin, Terry SP - 1 EP - 16 KW - semantic enhancements KW - Semantic tagging KW - Systematics KW - Taxonomy AB - Th e concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XMLtagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workfl ow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used. L2 - 44529 L3 - 45349 VL - 50 UR - http://pensoftonline.net/zookeys/index.php/journal/article/view/538/474 ER - TY - JOUR T1 - Bibliography of Family-group names in Diptera. JF - Myia Y1 - 1999 A1 - Thompson, F. Christian A1 - Evenhuis, Neal L. A1 - Sabrosky, Curtis W. SP - 361 EP - 576 L2 - 43874 L3 - 44410 VL - 10 UR - http://www.online-keys.net/sciaroidea/add01/Thompson_et_al_1999_family_group_names.pdf ER -