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

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

[email protected], http://epafilis.info

Associating Organisms With Their Environment:

Automated Mining, Assisted Curation and

Exploratory Visualization Approaches


Species – Environments


http://eol.org/data_objects/31415353

Information in Free Text


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


Literature Mining


processing text

to extract facts of interest


terrestrial, aquatic, marine, lagoon, coral reef, sediment, freshwater, soil


ENVIRONMENTS


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


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


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


EnvO parts Not included: species tissues foods

Limitations – Known Issues

negation not supported conflicts with anatomy terms

(e.g. mouth, blowhole)

Scope


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


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 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


Species – Environments


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/


http://eol.org/info/discover_what

•  Encyclopedia of Life (EOL) http://www.eol.org •  one-stop-shop for biodiversity knowledge •  Over 3 Mi Taxa


•  Encyclopedia of Life (EOL) http://www.eol.org •  one-stop-shop for biodiversity knowledge •  Over 3 Mi Taxa



ID: ENVO:00000192 Name: mudflat

ID: ENVO:00000020 Name: lake

http://eol.org/data_objects/31415353

Information in Free Text


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”)


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


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


Monthly Updates


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


other forms of access


Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Overview: http://eol.org/pages/913221

Quick Facts


Data Tab

Phoenicopterus ruber (Greater Flamingo) EOL Taxon Page Data Tab: http://eol.org/pages/913221 Parts of the screenshot truncated for illustration purposes


Integrated in Traitbank

http://eol.org/info/516 Parr CS, et al. TraitBank: Practical semantics for organism attribute data, Semantic Web Journal, under review


http://environments.hcmr.gr,http://environments.jensenlab.org


Command line


•  Interactive

•  Lightweight

•  Term look up assistant

•  Standards-compliant term suggestions


Prototype: http://environments.hcmr.gr/biocreative.html


https://gold.jgi-psf.org/studies?Study.Metagenomic+Study=Yes&Study.Is+Public=Yes

A

B

C



retroactive prospective


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


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.


large scale biological questions


citizen science project


When and where is a species

most likely to be found, and vice versa?


Which other species are most likely

to be found near by?


Where ? •  Location •  Environment type

When ? •  Life Stage •  Periods of year


too much data


Crete, Greece, http://www.gbif.org/occurrence/


•  ~15000 EnvO term tags in the EOL Pages •  For 234 bird species reported in Crete,

Greece (accord to GBIF, NCBI Taxonomy)


•  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]) 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]), http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/HEAPcloud_v0.1/


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


!  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


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


Digging-out Information

http://hartpurylrc.files.wordpress.com Photo by Dr Chatzinikolaou E


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)


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)

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

Data & Analytics

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