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BioDIP - a proposed infrastructure to link the taxonomic to the genomic and other domains
- 1. Donat Agosti Plazi agosti@plazi.org SSS Day 2015, November 6, NHMB, Bern BioDiP - a proposed infrastructure to link the taxonomic to the genomic and other domains
- 2. Content: What is the issue? Where do we stand? What is planned? What can you do?
- 3. Improve the Role of Published Biodiversity Literature in Policy decisions Published observation records (Scientific literature) EU BON Policy Brief
- 4. The Scientific Challenge: Annotate genes 1 tnntttccca cgaataaata atataagatt ttgattatta cctccttctt taattttatt 61 attatcaaga agattagttt ataaaggagt aggaacagga tgaactgttt atcctccttt 121 atctaataat ttatatcata atggattttc aactgattta gcaatttttt ctttacatat 181 tgcaggaata tcatcaatta taggagcaat taattttatt tcaacaattt taaatataca 241 tcataaaaat ttatcattag ataaaattcc attgttagtt tgatcaattt taattacagc 301 tattttatta ttattatctt tacctgtatt agcaggtgca attactatat tattaactga 361 tcgaaatcta aatacaactt tttttgatcc ttcgggtgga ggagatccaa ttttatatca 421 acatttattt
- 5. Text <tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="193329"/> <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie </tax:name> <tax:status>n. sp.</tax:status> Fig 1 D - F </tax:nomenclature> <tax:div type="description"> <tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margi to a sharp apical tooth, the apex parallel to the an (Holotype with material in mandibles, so mandibles a $ described below from paratypes.) Median clypeus .... </treatment> XML: Semantic enhanced text (e.g. TaxonX) From human to machine readable text RDF
- 6. Countries (Region) Australia (Queensland) Export species materials citations (DwC) Visualization of taxonomic literature
- 7. Text mining tools: Visualization of treatment content Summary of content of 37 Zootaxa spider publications and 8 Biodiversity Data Journal. (Miller et al., 2015)
- 8. Pseudomyrmex ants and Vachellia ant-acacias are a classic example of mutualism in biology. allenii melanoceras ruddiae chiapensis collinsii cookii cornigera globulifera hindsii janzenii mayana sphaerocephala boopis flavicornis hesperius ita janzeni kuenckeli mixtecus nigrocinctus nigropilosus opaciceps particeps peperi reconditus satanicus simulans spinicola subtilissimus veneficus ferrugineus gentlei gracilis Transbiotic link network Associated species linked through references in taxonomic treatments Acacia-ant species: Pseudomyrmex gracili Treatment: redescription Associated ant-acacia: Acacia gentlei Ants Plants Photocredits: Alex Wild Treatment Treatments linked through citations Text mining tools: Visualization of treatment content
- 9. The Scientific Challenge: link a name to its treatment
- 10. What is the issue? Build the necessary system A system that allows to text and data mine the corpus of taxonomic literature. A system that links taxonomic names to its treatments.
- 11. Trait information machine ready ResolutionReconciliation TreatmentBank NAMES MANAGEMENT CITATION MANAGEMENT REFBANK TREATMENT MANAGEMENT ATOMIZATION & SEMANTICIZATION OF CONTENT MARKUP / initial trait extraction Specialist taxonomic databases Build the necessary system
- 12. Where do we stand?
- 13. Number of citations: Better than most scientific papers The origin Where do we stand?
- 14. Citations of the ALL-Book (Google Scholar) Book 458 Chapter 1: Alonso, L.E., and D. Agosti. Biodiversity Studies, Monitoring, and Ants: An Overview 162 Chapter 2: Kaspari, M. A Primer in Ant Ecology (pdf) 85 Chapter 3: Andersen, A.N. A Global Ecology of Rainforest Ants: Functional Groups in Relation to Environmental Stress and Disturbance (pdf) 172 Chapter 4: Schultz, T.R., and T.P. McGlynn. The Interaction of Ants with Other Organisms (pdf) 94 Chapter 5: Brown, W.L.Jr. Diversity of Ants (pdf) 220 Chapter 6: Alonso, L.E. Ants as Indicators of Diversity (pdf) 164 Chapter 7: Kaspari, M., J.D. Majer. Using Ants to Monitor Environmental Change (pdf) 116 Chapter 8: Ward, P.S. Broad-scale Patterns of Diversity in Leaf litter Ant Communities (pdf) 112 Chapter 9: Bestelmeyer, B.T., D. Agosti, L.E. Alonso, C.R.F. Brandão, W.L. Brown Jr., J.H.C. Delabie, and R. Silvestre. Field Techniques for the Study of Ground-Dwelling Ants: An Overview, Description and Evaluation (pdf) 388 Chapter 10: Delabie, J.H.C., B.L. Fisher, J.D. Majer, and I.W. Wright. Sampling Effort and Choise of Methods (pdf) 117 Chapter 11: Lattke, J.E. Specimen Processing: Building and Curating an Ant Collection (pdf) 36 Chapter 12: Brandão, C.R.F. Major Regional and Type Collections of Ants (Formicidae) of the World and Sources for the Identification of Ant Species (pdf) 41 Chapter 13: Longino, J.R. What to Do with the Data (pdf) 89 Chapter 14: Agosti, D., and L.E. Alonso. The ALL Protocol: A Standard Protocol for the Collection of Ground- Dwelling Ants (pdf); versión en español (pdf) 179 Chapter 15: Fisher, B.L., A.K.F. Malsch, R. Gadagkar, J.H.C. Delabie, H.L. Vasconcelos, and J.D. Majer. Applying the ALL Protocol: Selected Case Studies (pdf); extended version (pdf) 21 Total 2454
- 15. Thanks to
- 16. Open Access Before antbase.org, Harvard‘s Museum of Comparative Zoology could claim to be the only location with a complete set of ant systematics publications from 1758 - present. Through antbase.org‘s digital library, access to this body of literature is worldwide, and it is actively used (>10,000 visits in one month only). 2004
- 17. .. Open Access to ca 80% of the papers citing the Antbook (most of if not through the publishers’ Websites. .. But it needs time to find the articles Thanks to Manual work
- 18. Access through Citation 2015 Zooke ys doi DOI: Digital Object Identifier
- 19. Create a citable open corpus of taxonomic publications
- 20. Create a citable open corpus of taxonomic publications Content (Nov 2015) Active: 4,500 Poctorupoidea and ant articles DOI provider for Revue Suisse de Zoologie, Israel Journal of Entomology, Polish Forestry Institute, Revue de Paléobiologie Pipeline: 5,000 ant articles 16,000 drosophilid articles All Pensoft journal articles, images, tables Planned: Back issues of RSZ Backbone for Plazi and Pensoft cited articles Participation: Please join! Make all Swiss based treatments accessible?
- 22. Biodiversity Literature Repository: RecordTreatment Illustration
- 23. Text <tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="193329"/> <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie </tax:name> <tax:status>n. sp.</tax:status> Fig 1 D - F </tax:nomenclature> <tax:div type="description"> <tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margi to a sharp apical tooth, the apex parallel to the an (Holotype with material in mandibles, so mandibles a $ described below from paratypes.) Median clypeus .... </treatment> XML: Semantic enhanced text (e.g. TaxonX) From human to machine readable text RDF
- 24. Taxonomic publication: deconstruct but keep parts linked Material citation TreatmentArticleJournal has part has part has part
- 25. Treatment: a well defined part of an article that defines the particular usage of a scientific name by an authority at a given time (a page(s) in a publication). Treatment The special case taxonomic literature: The citated elements are treatments, not article Formica obsoleta Linnaeus, 1758: 580
- 26. Treatment
- 27. Original combinations Reference to an orginal combination Subsequent useages of names cite the referenced treatment What is a treatment?
- 28. Treatment and treatment reference and citation Treatmentcitation Treatment references
- 29. Treatment Graph for the Malagasy Ants Aphaenogaster Original description Re-description cites cites/ synonymizes Re-description Re-de. Re-description cites
- 30. Material citation TreatmentArticleJournal is part of is part of is part of Taxonomic publication: deconstruct but keep parts linked
- 31. Material citationTreatmentArticleJournal is part of is part of is part of citescites cites Taxonomic publication: deconstruct but keep parts linked ISSN DOI httpURI httpURI
- 32. Material citationTreatmentArticleJournal is part of is part of is part of citescites cites Taxonomic publication: deconstruct but keep parts linked ISSN DOI httpURI httpURI CIEPS / ISSN CrossRef / DataCite Client Client Plazi PlaziBiodiversity Literature Repository / Zenodo CERN
- 33. Treatment Citation Life article treatment Dikow & Agosti, 2015.
- 34. Taxonomic publication Treatment Verbatim Material citations Specimen ID Treatment citation Bibliogr. citation Taxonomic Name Usages is part of cites Illustration
- 35. Taxonomic publication Material citation Genbank ID Collection Accession # Specimen ID Digital Object ID Collecting Event ID Host ID Verbatim is part of cites
- 36. Treatment: implicit and explicit links
- 37. Plazi Tools: Data extraction: tables «Treatment» Wissenschaftliche Artname Verbreitungsnachweis Cataglyphis tartessica workers Variable mean ± SD Head length 11.23 ± 0.12 Head width 11.15 ± 0.12 Scape length 11.47 ± 0.12 Mesosoma length 11.94 ± 0.16 Femur length 12.03 ± 0.14 Cephalic index 0 93.60 ± 3.940 Scape index 128.10 ± 7.660
- 38. Plazi tools: discovering of scientificnames
- 39. Plazi tools: discovering and parsing of bibliographicreferences
- 40. Plazi tools: discovering and parsing of observation data
- 41. Plazi tools: discovering of treatments
- 42. Status quo • 50,000+ treatments life, daily growth • RDF in Betaversion • GoldenGate Imagine (PDF and text mining tool) in betaversion • Provider for data for NCBI, Wikidata, GBIF, EOL, antweb • Biodiversity Literature Repository functional
- 45. article treatment Cites httpURI cites (DOI) Scientific name https://www.wikidata.org/wiki/ Property:P1992 Feed Wikipedia with taxonomic data
- 46. Status quo • 50,000+ treatments life, daily growth • RDF in Betaversion • GoldenGate Imagine (PDF and text mining tool) in betaversion • Provider for data for NCBI, Wikidata, GBIF, EOL, antweb • Biodiversity Literature Repository functional
- 47. What is planned? What can you do?
- 48. What is planned? What can you do? A system that allows to text and data mine the corpus of taxonomic literature. A system that links taxonomic names to its treatments.
- 49. Trait information machine ready ResolutionReconciliation TreatmentBank NAMES MANAGEMENT CITATION MANAGEMENT REFBANK TREATMENT MANAGEMENT ATOMIZATION & SEMANTICIZATION OF CONTENT MARKUP / initial trait extraction Specialist taxonomic databases What is planned? What can you do? existing prototype planned prototype
- 50. BioDiP Program: SUK-Programm 2013-2016 P-2 «Wissenschaftliche Information: Zugang, Verarbeitung und Speicherung» Partners: HES-SO, HEG Geneva (Swiss Institute of Bioinformatics), Plazi, open at various levels – from adding content to BLR to data mining and building applications Submission: February 2016 Duration: 2-3 years What is planned? What can you do?