2014 10 TDWG - Environments-EOL

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

*: pafilis@hcmr.gr, 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

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•  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

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

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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

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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

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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 (Umer.Ijaz@glasgow.ac.uk), 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 (Umer.Ijaz@glasgow.ac.uk), 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

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!  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

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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

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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)

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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/