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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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TDWG – 27th Oct 2014 – Jönköping
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, Lucia 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
*: [email protected], http://epafilis.info
TDWG – 27th Oct 2014 – Jönköping
Species – Environments
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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
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http://eol.org/info/discover_what
• Encyclopedia of Life (EOL) http://www.eol.org • one-stop-shop for biodiversity knowledge • Over 3 Mi Taxa
TDWG – 27th Oct 2014 – Jönköping
• Encyclopedia of Life (EOL) http://www.eol.org • one-stop-shop for biodiversity knowledge • Over 3 Mi Taxa
http://eol.org/info/discover_what
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Species Descriptions (e.g. “Biology Description”, “Ecology”, “Habitat”)
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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”)
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Information in Free Text
http://eol.org/data_objects/31415353
TDWG – 27th Oct 2014 – Jönköping
Information in Free Text
http://eol.org/data_objects/31415353
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Information in Free Text
ID: ENVO:00000192 Name: mudflat
ID: ENVO:00000020 Name: lake
http://eol.org/data_objects/31415353
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Literature Mining
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processing text
to extract facts of interest
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terrestrial, aquatic, marine, lagoon, coral reef, sediment, freshwater, soil
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ENVIRONMENTS
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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% 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. (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
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
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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
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EnvO parts Not included: species tissues foods
Limitations – Known Issues
negation not supported conflicts with anatomy terms
(e.g. mouth, blowhole)
Scope
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ENVIRONMENTS – Sample Output
Update to EOLTAGS 346289845
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 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
TDWG – 27th Oct 2014 – Jönköping
ENVIRONMENTS – Sample Output
Update to EOLTAGS 346289845
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 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
Traversing all IS_A, PART_OF
Relationships in EnvO
TDWG – 27th Oct 2014 – Jönköping
In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr
Monthly Updates
TDWG – 27th Oct 2014 – Jönköping
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
TDWG – 27th Oct 2014 – Jönköping
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
TDWG – 27th Oct 2014 – Jönköping
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
TDWG – 27th Oct 2014 – Jönköping
other forms of access
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In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr
http://eol.org/info/discover_what
TDWG – 27th Oct 2014 – Jönköping
In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr
Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Overview: http://eol.org/pages/913221
Quick Facts
TDWG – 27th Oct 2014 – Jönköping
In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr
Data Tab
Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Data Tab: http://eol.org/pages/913221 Parts of the screenshot truncated for illustration purposes
TDWG – 27th Oct 2014 – Jönköping
In collab.: Dr. Jennifer Hammock, Mr. Patrick Leary, Dr. Katja Schulz, Dr. Cyndy Parr
Integrated in Traitbank
http://eol.org/info/516 Parr CS, et al. TraitBank: Practical semantics for organism attribute data, Semantic Web Journal, under review
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large scale biological questions
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In collab.: Prof. Rob Stevenson (UMass)
citizen science project
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In collab.: Prof. Rob Stevenson (UMass)
When and where is a species
most likely to be found, and vice versa?
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Which other species are most likely
to be found near by?
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In collab.: Prof. Rob Stevenson (UMass)
Where ? • Location • Environment type
When ? • Life Stage • Periods of year
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too much data
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Crete, Greece, http://www.gbif.org/occurrence/
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• ~15000 EnvO term tags in the EOL Pages • For 234 bird species reported in Crete,
Greece (accord to GBIF, NCBI Taxonomy)
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• Statistics (e.g term count per taxon) • Data provenance (e.g. EOL Text Type) • Taxonomy • Interactive Visualizations
Developed by Dr. Umer Ijaz, University of Glasgow ([email protected]), source: 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
Developed by Dr. Umer Ijaz, University of Glasgow ([email protected]), source: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/HEAPcloud_v0.1/
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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
TDWG – 27th Oct 2014 – Jönköping
! 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
! 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
Summary
TDWG – 27th Oct 2014 – Jönköping
Based on processing PubMed, Apr 2013
Co-mention based analysis More Entity types • Functional Traits (feeding type, body features, etc) • Localities (co-ordindates, geographical locations)
Next Steps
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Digging-out Information
http://hartpurylrc.files.wordpress.com Photo by Dr Chatzinikolaou E
TDWG – 27th Oct 2014 – Jönköping
Acknowledgements
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)
Thank You!
Amvrakikos Lagoons, May 2011
ACTION ES1103
TDWG – 27th Oct 2014 – Jönköping
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 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
E600 Corpus
• 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)
http://environments-eol.blogspot.gr/
![abacus abacas [MATA] · Web viewreproductive system córas atáirgthe [EOL.] reptile reiptíl [EOL.] resource acmhainn; natural resources acmhainní nádúrtha [EOL.] respiration](https://img.pdfslide.net/doc/110x75/603e4ae368bd0d456c0be828/abacus-abacas-mata-web-view-reproductive-system-cras-atirgthe-eol-reptile.jpg)
