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EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Evangelos Pafilis
Institute of Marine Biology, Biotechnology and Aquac...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Species – Environments
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://eol.org/data_objects/31415353
Information in Free Text
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://eol.org/data_objects/31415353
Information in Free Text
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Microbes are key players in both healthy and degraded coral reefs.
A c...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Microbes are key players in both healthy and degraded coral reefs.
A c...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Literature Mining
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
processing text
to extract facts of interest
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
terrestrial, aquatic,
marine, lagoon, coral reef,
sediment, freshwater...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENVIRONMENTS
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENVIRONMENTS
http://environments.hcmr.gr
http://environments-eol.blogs...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
biome
environmental
feature
environmental
material
environmental
condi...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENVIRONMENTS – Improving Accuracy
●  Increasing matches in text
●  ort...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
EnvO parts Not included:
species
tissues
foods
Limitations – Known Iss...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENVIRONMENTS – Sample Output
eol_documents_ascii_nonHTML.txt 346289845...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENVIRONMENTS – Sample Output
eol_documents_ascii_nonHTML.txt 346289845...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Species – Environments
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Parr CS, et al. The Encyclopedia of Life v2: Providing Global Access t...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://eol.org/info/discover_what
•  Encyclopedia of Life (EOL) http:/...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
•  Encyclopedia of Life (EOL) http://www.eol.org
•  one-stop-shop for ...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ID: ENVO:00000192
Name: mudflat
ID: ENVO:00000020
Name: lake
http://eo...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://rs.tdwg.org/ontology/voc/SPMInfoItems#Biology
http://rs.tdwg.or...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENV-EOL Annotation .tsv
EOL:913221 31415353;http://rs.tdwg.org/ontolog...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
ENV-EOL Annotation .tsv
EOL:913221 31415353;http://rs.tdwg.org/ontolog...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Monthly Updates
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Download
ENVIRONMENTS-EOL Annotations (17th Oct 2014)
•  234.582 EOL T...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
other forms of access
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://eol.org/info/discover_what
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Overview: http:...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Data Tab
Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Data T...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Integrated in Traitbank
http://eol.org/info/516Parr CS, et al. TraitBa...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://environments.hcmr.gr,
http://environments.jensenlab.org
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Command line
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
•  Interactive
•  Lightweight
•  Term look up assistant
•  Standards-c...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Prototype: http://environments.hcmr.gr/biocreative.html
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
https://gold.jgi-psf.org/studies?Study.Metagenomic+Study=Yes&Study.Is+...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Prototype: http://environments.hcmr.gr/biocreative.html
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Prototype: http://environments.hcmr.gr/biocreative.html
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Prototype: http://environments.hcmr.gr/biocreative.html
retroactive
pr...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
BioCreative V Track 5: Interactive Curation (IAT)
Dr. L. Hirschman, Dr...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
http://jensenlab.org/
http://tissues.jensenlab.org/ - Santos A et al.,...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
large scale biological questions
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
citizen science project
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
When and where is a species
most likely to be found, and vice versa?
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Which other species are most likely
to be found near by?
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Where ?
•  Location
•  Environment type
When ?
•  Life Stage
•  Period...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
too much data
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Crete, Greece, http://www.gbif.org/occurrence/
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
•  ~15000 EnvO term tags in the EOL Pages
•  For 234 bird species repo...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
•  Statistics (e.g term count per taxon)
•  Data provenance (e.g. EOL ...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.a...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.a...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Specific text sources to address specific biological questions
http://...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
!  Species – Environment association
!  ENVIRONMENTS:
!  Dictionary-ba...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Based on processing PubMed, Apr 2013
Co-mention based analysis
Visuali...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Digging-out Information
http://hartpurylrc.files.wordpress.comPhoto by...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Acknowledgements
Amvrakikos Lagoons, May 2011
ACTION ES1103
Thank You!...
EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece
Acknowledgements
Thank You!
Amvrakikos Lagoons, May 2011
ACTION ES1103...
2015 06 hcmr - emodnet-eubon  - associating organisms with their environments - low res
2015 06 hcmr - emodnet-eubon  - associating organisms with their environments - low res
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2015 06 hcmr - emodnet-eubon - associating organisms with their environments - low res

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Associating organisms with their environment:
Automated, assisted curation and visualisation approaches

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2015 06 hcmr - emodnet-eubon - associating organisms with their environments - low res

  1. 1. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Evangelos Pafilis Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece pafilis@hcmr.gr, http://epafilis.info Associating Organisms With Their Environment: Automated Mining, Assisted Curation and Exploratory Visualization Approaches
  2. 2. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Species – Environments
  3. 3. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://eol.org/data_objects/31415353 Information in Free Text
  4. 4. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://eol.org/data_objects/31415353 Information in Free Text
  5. 5. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Source: http://metagenomics.anl.gov/linkin.cgi?metagenome=4440039.3 (“Project Description”, Dinsdale et al, 2008) Microbial mat samples were collected from the hydrothermal vent field located in the Kolumbo submarine volcanic crater, off the coast of the island of Santorini. The bacteria and archaea community composition was evaluated further via shotgun metagenomics analysis In-house HCMR document (Polymenakou, Oulas, et al.) Source: http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12264/full (Lagostina et al., 2015) Figure 1. Sampling sites on a cross-slope transect. [….] Oceanographically, the stations represent the abyssal plain (GeoB12815), the continental rise (GeoB12808, GeoB12811), the continental slope (GeoB12803, GeoB12802), the shelf break (GeoB12807) and the shelf (GeoB12806). Surface sediments were recovered by gravity and multi-coring. [.…] Scientific web pages Literature (abstracts, full-text articles, legends) In-house documents
  6. 6. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Source: http://metagenomics.anl.gov/linkin.cgi?metagenome=4440039.3 (“Project Description”, Dinsdale et al, 2008) Microbial mat samples were collected from the hydrothermal vent field located in the Kolumbo submarine volcanic crater, off the coast of the island of Santorini. The bacteria and archaea community composition was evaluated further via shotgun metagenomics analysis In-house HCMR document (Polymenakou, Oulas, et al.) Source: http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12264/full (Lagostina et al., 2015) Figure 1. Sampling sites on a cross-slope transect. [….] Oceanographically, the stations represent the abyssal plain (GeoB12815), the continental rise (GeoB12808, GeoB12811), the continental slope (GeoB12803, GeoB12802), the shelf break (GeoB12807) and the shelf (GeoB12806). Surface sediments were recovered by gravity and multi-coring. [.…] Scientific web pages Literature (abstracts, full-text articles, legends) In-house documents
  7. 7. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Literature Mining
  8. 8. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece processing text to extract facts of interest
  9. 9. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece terrestrial, aquatic, marine, lagoon, coral reef, sediment, freshwater, soil
  10. 10. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece ENVIRONMENTS
  11. 11. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece ENVIRONMENTS http://environments.hcmr.gr http://environments-eol.blogspot.gr/ ●  Dictionary based, Open Source ●  Environment Ontology ●  Fast (4000 PubMed abstracts / sec) * ●  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% 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 Pafilis,E. et al. (2015) ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, 10.1093/bioinformatics/btv045
  12. 12. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece biome environmental feature environmental material environmental condition habitat … … … … … Based on slides by Dr. Pier Luigi Buttigier, AWI, Bremenhaven, Germany http://environmentontology.org ~1600 terms, June 2013 EnvO: source of environment descriptor names and synonyms
  13. 13. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece 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) ●  Preventing overmatching (i.e. avoiding increased FP) ●  „stopword-list” (e.g. spring, well, range) Action Example 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
  14. 14. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece EnvO parts Not included: species tissues foods Limitations – Known Issues negation not supported conflicts with anatomy terms (e.g. mouth, blowhole) Scope
  15. 15. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece 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 File Name Start offset End offset 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
  16. 16. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece 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 File Name Start offset End offset 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 Traversing all IS_A, PART_OF Relationships in EnvO
  17. 17. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Species – Environments
  18. 18. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Parr CS, et al. The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth (2014) Biodiversity Data Journal 2: e1079 http://eol.org/
  19. 19. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://eol.org/info/discover_what •  Encyclopedia of Life (EOL) http://www.eol.org •  one-stop-shop for biodiversity knowledge •  Over 3 Mi Taxa
  20. 20. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece •  Encyclopedia of Life (EOL) http://www.eol.org •  one-stop-shop for biodiversity knowledge •  Over 3 Mi Taxa http://eol.org/info/discover_what
  21. 21. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece ID: ENVO:00000192 Name: mudflat ID: ENVO:00000020 Name: lake http://eol.org/data_objects/31415353 Information in Free Text
  22. 22. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece 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”) Species Descriptions (e.g. “Biology Description”, “Ecology”, “Habitat”)
  23. 23. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece ENV-EOL Annotation .tsv 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 EOL Taxon ID EOL Data Object EnvO ID Traversing all IS_A, PART_OF Relationships in EnvO Subject Type Match text 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. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece ENV-EOL Annotation .tsv 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 EOL Taxon ID EOL Data Object EnvO ID Direct Matches Only (No hierarchy traversal) Subject Type Match text 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
  25. 25. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Monthly Updates
  26. 26. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Download ENVIRONMENTS-EOL Annotations (17th Oct 2014) •  234.582 EOL Taxa •  1.945.383 Tags •  1.077.522 Unique EOL Taxon – EnvO ID pairs 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
  27. 27. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece other forms of access
  28. 28. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://eol.org/info/discover_what
  29. 29. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Overview: http://eol.org/pages/913221 Quick Facts
  30. 30. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Data Tab Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Data Tab: http://eol.org/pages/913221 Parts of the screenshot truncated for illustration purposes
  31. 31. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Integrated in Traitbank http://eol.org/info/516Parr CS, et al. TraitBank: Practical semantics for organism attribute data, Semantic Web Journal, under review
  32. 32. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://environments.hcmr.gr, http://environments.jensenlab.org
  33. 33. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Command line
  34. 34. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece •  Interactive •  Lightweight •  Term look up assistant •  Standards-compliant term suggestions
  35. 35. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Prototype: http://environments.hcmr.gr/biocreative.html
  36. 36. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece https://gold.jgi-psf.org/studies?Study.Metagenomic+Study=Yes&Study.Is+Public=Yes A B C
  37. 37. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Prototype: http://environments.hcmr.gr/biocreative.html
  38. 38. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Prototype: http://environments.hcmr.gr/biocreative.html
  39. 39. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Prototype: http://environments.hcmr.gr/biocreative.html retroactive prospective
  40. 40. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece BioCreative V Track 5: Interactive Curation (IAT) Dr. L. Hirschman, Dr. C. Arighi et al. September 2015, Sevilla, Spain Beta: •  Entity highlighting •  Suggested Term: •  sorting •  Selection •  exporting •  Integration with Metagenomics Resources
  41. 41. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece http://jensenlab.org/ http://tissues.jensenlab.org/ - Santos A et al., PeerJ in press preprint: http://biorxiv.org/content/early/2014/11/10/010975 http://diseases.jensenlab.org/ - Pletscher-Frankild,S., et al. (2014) DISEASES: Text mining and data integration of disease- gene associations. Methods, 74, 83–89.
  42. 42. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece large scale biological questions
  43. 43. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece citizen science project
  44. 44. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece When and where is a species most likely to be found, and vice versa?
  45. 45. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Which other species are most likely to be found near by?
  46. 46. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Where ? •  Location •  Environment type When ? •  Life Stage •  Periods of year
  47. 47. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece too much data
  48. 48. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Crete, Greece, http://www.gbif.org/occurrence/
  49. 49. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece •  ~15000 EnvO term tags in the EOL Pages •  For 234 bird species reported in Crete, Greece (accord to GBIF, NCBI Taxonomy)
  50. 50. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece •  Statistics (e.g term count per taxon) •  Data provenance (e.g. EOL Text Type) •  Taxonomy •  Interactive Visualizations
  51. 51. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.ac.uk) http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/summarize_v0.2/summarize.html Try it live: http:// environments.hcmr.gr/ cretan-birds/ summarize.html
  52. 52. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Developed by Dr. Umer Ijaz, University of Glasgow (Umer.Ijaz@glasgow.ac.uk), http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/HEAPcloud_v0.1/
  53. 53. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece 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 Further Inspection
  54. 54. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece !  Species – Environment association !  ENVIRONMENTS: !  Dictionary-based environment descriptive term identification !  Ontological Community standards, e.g. EnvO: name source !  EOL: global aggregator of biodiversity knowledge !  Semantically typed text clauses !  ENVIRONMENTS and EOL !  processing the EOL Taxon pages to extractenvironment descriptors !  Raw annotations (tabular format) !  Browse via the EOL Web Interface (Broad audience) !  Search and Retrieve via TraitBank@EOL !  Extract: standard compliant environement term suggestion !  Lightweight interactive browsing escort !  Process user selected text !  Simple and generic annotation retrieval !  Large scale biological questions !  Integrative data analysis / interactive visualization !  Citizen science project support Summary
  55. 55. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Based on processing PubMed, Apr 2013 Co-mention based analysis Visualization – incorporate in community resources LifeWatchGreece - RvLab More Entity types (depending on resources) •  Functional Traits (feeding type, body features, etc) •  Localities (co-ordindates, geographical locations) Next Steps
  56. 56. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Digging-out Information http://hartpurylrc.files.wordpress.comPhoto by Dr Chatzinikolaou E
  57. 57. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Acknowledgements Amvrakikos Lagoons, May 2011 ACTION ES1103 Thank You! HCMR-IMBG: Christos Arvanitidis, Christina Pavloudi, Katerina Vasileiadou, Lucia Fanini, Sarah Faulwetter, Anastasis Oulas, Alexandros Gkougkousis et al. (RvLAB) 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, E Pereira, AWI: Dr P. Buttigieg BioCreative: Dr. L. Hirschman (MITRE, DoE Award No DE-SC0010838) SEQenv (https://bitbucket.org/seqenv), Reflect (http://reflect.ws) Genomes OnLine Database, Virome / Metagenomes Online Funding: EOL Rubenstein Fellowship, LifeWatc Greece, MARBIGEN, NNF-CPR, EOL-BHL NESCent Researh, Sprint 2014,”SEQenv” Hackathons (COST ES1103)
  58. 58. EMDONET/EUBON – 10th June 2015 – HCMR, Crete Greece Acknowledgements Thank You! Amvrakikos Lagoons, May 2011 ACTION ES1103 id: ENVO:00000038 name: lagoon HCMR-IMBG: Christos Arvanitidis, Christina Pavloudi, Katerina Vasileiadou, Lucia Fanini, Sarah Faulwetter, Anastasis Oulas, Alexandros Gkougkousis et al. (RvLAB) 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, E Pereira, AWI: Dr P. Buttigieg BioCreative: Dr. L. Hirschman (MITRE, DoE Award No DE-SC0010838) SEQenv (https://bitbucket.org/seqenv), Reflect (http://reflect.ws) Genomes OnLine Database, Virome / Metagenomes Online Funding: EOL Rubenstein Fellowship, LifeWatc Greece, MARBIGEN, NNF-CPR, EOL-BHL NESCent Researh, Sprint 2014,”SEQenv” Hackathons (COST ES1103)

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