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2014 10 TDWG - Environments-EOL

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Identification of Environment Ontology terms in text and
the annotation of the Encyclopedia of Life
http://www.environments-eol.blogspot.com/

Evangelos Pafilis1*, Sune Frankild2, Lu cia Fanini1, Sarah Faulwetter1, Christina
Pavloudi1, Julia Schnetzer3, Aikaterini Vasileiadou1, Umer Ijaz4, Christos Arvanitidis1,
Robert Stevenson5, Lars Juhl Jensen2

1HCMR, Crete, GR, 2CPR-NNF, Copenhagen, DK, 3MPI-MM, Bremen, DE, 4Uni of Glasgow, UK, 5Uni of
Massachusetts, Boston, US

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2014 10 TDWG - Environments-EOL

  1. 1. Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life http://www.environments-eol.blogspot.com/ Evangelos Pafilis1*, Sune Frankild2, Lu cia Fanini1, Sarah Faulwetter1, Christina Pavloudi1, Julia Schnetzer3, Aikaterini Vasileiadou1, Umer Ijaz4, Christos Arvanitidis1, Robert Stevenson5, Lars Juhl Jensen2, 1HCMR, Crete, GR, 2CPR-NNF, Copenhagen, DK, 3MPI-MM, Bremen, DE, 4Uni of Glasgow, UK, 5Uni of Massachusetts, Boston, US *: pafilis@hcmr.gr, http://epafilis.info TDWG – 27th Oct 2014 – Jönköping
  2. 2. Species – Environments TDWG – 27th Oct 2014 – Jönköping
  3. 3. http://eol.org/ Parr CS, et al. The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth (2014) Biodiversity Data Journal 2: e1079 TDWG – 27th Oct 2014 – Jönköping
  4. 4. • Encyclopedia of Life (EOL) http://www.eol.org • one-stop-shop for biodiversity knowledge • Over 3 Mi Taxa http://eol.org/info/discover_what TDWG – 27th Oct 2014 – Jönköping
  5. 5. • Encyclopedia of Life (EOL) http://www.eol.org • one-stop-shop for biodiversity knowledge • Over 3 Mi Taxa http://eol.org/info/discover_what TDWG – 27th Oct 2014 – Jönköping
  6. 6. Species Descriptions (e.g. “Biology Description”, “Ecology”, “Habitat”) TDWG – 27th Oct 2014 – Jönköping
  7. 7. Species Descriptions (e.g. “Biology Description”, “Ecology”, “Habitat”) http://rs.tdwg.org/ontology/voc/SPMInfoItems#Biology http://rs.tdwg.org/ontology/voc/SPMInfoItems#Conservation http://rs.tdwg.org/ontology/voc/SPMInfoItems#Description http://rs.tdwg.org/ontology/voc/SPMInfoItems#Dispersal http://rs.tdwg.org/ontology/voc/SPMInfoItems#Distribution http://rs.tdwg.org/ontology/voc/SPMInfoItems#Ecology http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat http://rs.tdwg.org/ontology/voc/SPMInfoItems#LifeCycle http://rs.tdwg.org/ontology/voc/SPMInfoItems#Migration http://rs.tdwg.org/ontology/voc/SPMInfoItems#Reproduction http://rs.tdwg.org/ontology/voc/SPMInfoItems#TrophicStrategy http://www.eol.org/voc/table_of_contents#Wikipedia More info: http://eol.org/info/98 (“EOL Subject Types”) TDWG – 27th Oct 2014 – Jönköping
  8. 8. Information in Free Text http://eol.org/data_objects/31415353 TDWG – 27th Oct 2014 – Jönköping
  9. 9. Information in Free Text http://eol.org/data_objects/31415353 TDWG – 27th Oct 2014 – Jönköping
  10. 10. Information in Free Text TDWG – 27th Oct 2014 – Jönköping ID: ENVO:00000192 Name: mudflat ID: ENVO:00000020 Name: lake http://eol.org/data_objects/31415353
  11. 11. Literature Mining TDWG – 27th Oct 2014 – Jönköping
  12. 12. processing text to extract facts of interest TDWG – 27th Oct 2014 – Jönköping
  13. 13. terrestrial, aquatic, marine, lagoon, coral reef, sediment, freshwater, soil TDWG – 27th Oct 2014 – Jönköping
  14. 14. ENVIRONMENTS TDWG – 27th Oct 2014 – Jönköping
  15. 15. ENVIRONMENTS http://environments.hcmr.gr http://environments-eol.blogspot.gr/ ● Dictionary based, Open source ● Environment Ontology ● fast performance ● 4000 PubMed abstracts / second * ● Based on SPECIES name recognition tagger (Pafilis et al, PLOS ONE) ● E600 gold standard: EnvO-based corpus of EOL Species pages ● Recognition Accuracy – Mention Level: - F1: 82.0% Pafilis E et al. (2013) The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. PLoS ONE 8(6): e65390 TDWG – 27th Oct 2014 – Jönköping 87.1% of the TPs: exact id among predicted ones *: based a single-thread run on an Intel 2,27GHz, 24 GB RAM processing a set of 536,052 abstracts
  16. 16. EnvO: source of environment descriptor names and synonyms biome environmental feature environmental material environmental condition … … … habitat … http://environmentontology.org ~1600 terms, June 2013 TDWG – 27th Oct 2014 – Jönköping … Based on slides by Dr. Pier Luigi Buttigier, AWI, Bremenhaven, Germany
  17. 17. ENVIRONMENTS – Improving Accuracy ● Increasing matches in text ● orthographic variation supported e.g. freshwater, fresh water, and fresh-water ● Case-insensitive matching ● Synonym generation to reflect the way environment descriptive terms are mentioned in text (both generic and EnvO specific) Action Example ● Preventing overmatching (i.e. avoiding increased FP) ● „stopword-list” (e.g. spring, well, range) TDWG – 27th Oct 2014 – Jönköping Add a variant in which non-informative words have been removed epipelagic zone → epipelagic estuarine biome → estuarine Plural form addition sediment → sediments Adjective form addition lagoon → lagoonal
  18. 18. Scope EnvO parts Not included: species tissues foods Limitations – Known Issues negation not supported conflicts with anatomy terms (e.g. mouth, blowhole) TDWG – 27th Oct 2014 – Jönköping
  19. 19. ENVIRONMENTS – Sample Output eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000192 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00002297 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000043 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000000 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000012 eol_documents_ascii_nonHTML.txt 346289871 346289873 mud ENVO:01000001 eol_documents_ascii_nonHTML.txt 346289871 346289873 mud ENVO:00010483 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000180 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000191 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00002297 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000176 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000000 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000477 TDWG – 27th Oct 2014 – Jönköping File Name Start coord End coord Match text EnvO ID Tags corresponding to “Habitat” text data object: http://eol.org/data_objects/31415353 of EOL Taxon Phoenicopterus ruber (Greater Flamingo): http://eol.org/pages/913221
  20. 20. ENVIRONMENTS – Sample Output eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000192 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00002297 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000043 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000000 eol_documents_ascii_nonHTML.txt 346289845 346289853 mud flats ENVO:00000012 eol_documents_ascii_nonHTML.txt 346289871 346289873 mud ENVO:01000001 eol_documents_ascii_nonHTML.txt 346289871 346289873 mud ENVO:00010483 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000180 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000191 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00002297 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000176 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000000 eol_documents_ascii_nonHTML.txt 346289905 346289910 mounds ENVO:00000477 TDWG – 27th Oct 2014 – Jönköping File Name Start coord End coord Match text EnvO ID Traversing all IS_A, PART_OF Relationships in EnvO Tags corresponding to “Habitat” text data object: http://eol.org/data_objects/31415353 of EOL Taxon Phoenicopterus ruber (Greater Flamingo): http://eol.org/pages/913221
  21. 21. Monthly Updates In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr TDWG – 27th Oct 2014 – Jönköping
  22. 22. ENV-EOL Annotation .tsv Subject Type Match text EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000192 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00002297 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000043 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000000 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000012 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud ENVO:01000001 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud ENVO:00010483 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000180 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000191 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00002297 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000176 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000000 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000477 TDWG – 27th Oct 2014 – Jönköping EOL Taxon ID EOL Data Object EnvO ID Traversing all IS_A, PART_OF Relationships in EnvO Annotations corresponding to “Habitat” text data object: http://eol.org/data_objects/31415353 of EOL Taxon Phoenicopterus ruber (Greater Flamingo): http://eol.org/pages/913221
  23. 23. ENV-EOL Annotation .tsv Subject Type Match text EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000192 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud ENVO:01000001 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mounds ENVO:00000180 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat mud flats ENVO:00000192 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat estuaries ENVO:00000045 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat bodies of water ENVO:00000063 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat coastal areas ENVO:00000303 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat inlets ENVO:00000475 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat rivers ENVO:00000887 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat rivers ENVO:00000890 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat lakes ENVO:00000020 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat coastal ENVO:00000303 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat lagoons ENVO:00000038 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat volcanic ENVO:00000354 EOL:913221 31415353;http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat lakes ENVO:00000020 TDWG – 27th Oct 2014 – Jönköping EOL Taxon ID EOL Data Object EnvO ID Direct Matches Only (No hierarchy traversal) Annotations corresponding to “Habitat” text data object: http://eol.org/data_objects/31415353 of EOL Taxon Phoenicopterus ruber (Greater Flamingo): http://eol.org/pages/913221
  24. 24. Download ENVIRONMENTS-EOL Annotations (17th Oct 2014) • 234.582 EOL Taxa • 1.945.383 Tags • 1.077.522 Unique EOL Taxon – EnvO ID pairs TDWG – 27th Oct 2014 – Jönköping ENVIRONMENTS • Home Page: http://environments.hcmr.gr/ • ENVIRONMENTS-EOL Annotations: http://download.jensenlab.org/EOL/ • Tagger Software: http://download.jensenlab.org/environments_tagger.tar.gz
  25. 25. other forms of access TDWG – 27th Oct 2014 – Jönköping
  26. 26. http://eol.org/info/discover_what In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr TDWG – 27th Oct 2014 – Jönköping
  27. 27. Quick Facts Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Overview: http://eol.org/pages/913221 In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr TDWG – 27th Oct 2014 – Jönköping
  28. 28. Data Tab Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Data Tab: http://eol.org/pages/913221 Parts of the screenshot truncated for illustration purposes In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr TDWG – 27th Oct 2014 – Jönköping
  29. 29. Integrated in Traitbank http://Parr CS, et al. TraitBank: Practical semantics for organism eol.org/info/516 attribute data, Semantic Web Journal, under review In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr TDWG – 27th Oct 2014 – Jönköping
  30. 30. large scale biological questions TDWG – 27th Oct 2014 – Jönköping
  31. 31. citizen science project In collab.: Prof. Rob Stevenson (UMass) TDWG – 27th Oct 2014 – Jönköping
  32. 32. When and where is a species most likely to be found, and vice versa? In collab.: Prof. Rob Stevenson (UMass) TDWG – 27th Oct 2014 – Jönköping
  33. 33. Which other species are most likely to be found near by? TDWG – 27th Oct 2014 – Jönköping
  34. 34. Where ? • Location • Environment type When ? • Life Stage • Periods of year In collab.: Prof. Rob Stevenson (UMass) TDWG – 27th Oct 2014 – Jönköping
  35. 35. too much data TDWG – 27th Oct 2014 – Jönköping
  36. 36. Crete, Greece, http://www.gbif.org/occurrence/ TDWG – 27th Oct 2014 – Jönköping
  37. 37. • ~15000 EnvO term tags in the EOL Pages • For 234 bird species reported in Crete, Greece (accord to GBIF, NCBI Taxonomy) TDWG – 27th Oct 2014 – Jönköping
  38. 38. • Statistics (e.g term count per taxon) • Data provenance (e.g. EOL Text Type) • Taxonomy • Interactive Visualizations TDWG – 27th Oct 2014 – Jönköping
  39. 39. Try it live: http:// environments.hcmr.gr/ cretan-birds/ summarize.html Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.ac.uk), source: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/summarize_v0.2/summarize.html
  40. 40. Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.ac.uk), source: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/HEAPcloud_v0.1/
  41. 41. Further Inspection Specific text sources to address specific biological questions http://rs.tdwg.org/ontology/voc/SPMInfoItems#Habitat http://rs.tdwg.org/ontology/voc/SPMInfoItems#Migration http://rs.tdwg.org/ontology/voc/SPMInfoItems#Reproduction http://rs.tdwg.org/ontology/voc/SPMInfoItems#TrophicStrategy Hierarchy of ontological data structures e.g. habitat only, environmental material only , environmental feature only Taxonomy e.g. re-calculate term counts at the family or higher level taxon TDWG – 27th Oct 2014 – Jönköping
  42. 42. Summary ! Species – Environment association ! EOL: global aggregator of biodiversity knowledge ! Semantically typed text clauses ! ENVIRONMENTS: ! Dictionary-based environment descriptive term identification ! Ontological Community standards, e.g. EnvO: name source ! ENVIRONMENTS and EOL ! processing the EOL Taxon pages ! extract descriptions of their environmental context TDWG – 27th Oct 2014 – Jönköping ! Data Access ! Raw annotations (tabular format) ! Browse via the EOL Web Interface (Broad audience) ! Search and Retrieve via TraitBank@EOL ! Large scale biological questions ! Integrative data analysis / interactive visualization ! Citizen science project support
  43. 43. Next Steps Co-mention based analysis Based on processing PubMed, Apr 2013 More Entity types • Functional Traits (feeding type, body features, etc) • Localities (co-ordindates, geographical locations) TDWG – 27th Oct 2014 – Jönköping
  44. 44. Digging-out Information http://hartpurylrc.Photo by Dr Chatzinikolaou E files.wordpress.com TDWG – 27th Oct 2014 – Jönköping
  45. 45. Acknowledgements Thank You! HCMR-IMBG: Christos Arvanitidis, Christina Pavloudi, Katerina Vasileiadou Lucia Fanini, Sarah Faulwetter, Anastasis Oulas NNF CPR: Lars Juhl Jensen, Sune Frankild U Mass: Rob Stevenson Uni Glasgow: Christopher Quince, Umer Ijaz EOL: Cynthia Parr, Jennifer Hammock, Patrick Leary, Katja Schulz MM-MPI: J. Schnetzer, AWI: Dr P. Buttigieg, and more Funding: EOL Rubenstein Fellowship, LifeWatch Greece, MARBIGEN, NNF-CPR, EOL-BHL NESCent Researh, Sprint 2014,”SEQenv” Hackathons (COST ES1103) TDWG – 27th Oct 2014 – Jönköping Amvrakikos Lagoons, May 2011 ACTION ES1103
  46. 46. Acknowledgements Thank You! HCMR-IMBG: Christos Arvanitidis, Christina Pavloudi, Katerina Vasileiadou TDWG – 27th Oct 2014 – Jönköping id: ENVO:00000038 name: lagoon Amvrakikos Lagoons, May 2011 ACTION ES1103 Lucia Fanini, Sarah Faulwetter, Anastasis Oulas NNF CPR: Lars Juhl Jensen, Sune Frankild U Mass: Rob Stevenson Uni Glasgow: Christopher Quince, Umer Ijaz EOL: Cynthia Parr, Jennifer Hammock, Patrick Leary, Katja Schulz MM-MPI: J. Schnetzer, AWI: Dr P. Buttigieg, and more Funding: EOL Rubenstein Fellowship, LifeWatch Greece, MARBIGEN, NNF-CPR, EOL-BHL NESCent Researh, Sprint 2014,”SEQenv” Hackathons (COST ES1103)
  47. 47. E600 Corpus http://environments-eol.blogspot.gr/ • 600 EOL species pages • Sections like “Habitat”, “Ecology”, “Reproduction”, “Distribution” • randomly picked from the following eight taxonomic taxa: Actinopterygii, Annelida, Arthropoda, Aves, Chlorophyta, Mammalia, Mollusca, Streptophyta. • 6 curators (4 graduate students, 2 postdocs) TDWG – 27th Oct 2014 – Jönköping

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