Friday, March 7, 2014

November 2013 - February 2014: EOL/Traitbank Integration, On-going Benchmark, Exploratory Visualizations

Unlike the silence of this blog, progress has occurred in all fronts of the ENVIRONMENTS-EOL project. Many sub-parts of which are now either finished, or nearing completion.

Have you seen ENVIRONMENTS-EOL predictions in the Encyclopedia of Life?

Early in 2014 the Encyclopedia of Life (EOL) released its new version, along with Traitbank, its novel data search facility. Among other innovative biodiversity research features, Jennifer Hammock, Patrick Leary, Katja Schulz, Cyndy Parr (and anyone else I may be omitting) have incorporated ENVIRONMENTS-EOL predictions into the EOL system.

As shown on the left Environment Ontology (ENVO) descriptive terms associated with a taxon (in this example: Hexanchus griseus, the Bluntnose Six-gill Shark), can be seen both in the Overview, Quick Facts (short list, upper-right part of the figure), and under the Data Tab (extended list, lower-right part of the figure).

Such features render the ENVIRONMENTS-EOL predictions accessible for all EOL users indifferent of the Information Technology skills.

Due to natural language intricacies, such as the multiple meanings a word may have, erroneous predictions will occur. As described in previous posts (April, July 2013), ENVIRONMENTS-EOL has been developed in iterative cycles aiming to identify and handle the most prominent of such errors.

An improved version of the ENVIRONMENTS tagger is now ready and the release of a new ENVIRONMENTS-EOL annotation dataset is in preparation.

Named Entity Recognition (NER) Evaluation
In a text-mining point-of-view, the work on the ENVIRONMENTS-600 corpus has been concluded; the Inter Annotator Agreement having been the last step of the process.

The tagger evaluation in terms of precision and recall is nearly complete. Points of particular interest were:
  • the handling of multiple EnvO identifiers having been mapped to a term by the curators, and/or being returned by the tagger
  • the hierarchical relationship of curated/predicted terms according to EnvO
  • the NER evaluation for distinct EnvO sub-graphs only (e.g. only for environmental features, or habitats, or environmental materials)
  • the NER evaluation for the different EOL Species page sections (e.g. only for "Habitat", or "Distribution", or "Taxon Biology")
The analysis of the NER performance is on-going.

North, South America bird habitat associations and vizualisations
Early in February 2014, the NESCent EOL-BHL Research Sprint (Durham, North Carolina) event gave ENVIRONMENTS-EOL a unique opportunity to explore concrete biological questions based on its machinery.

Interdisciplinary collaboration was the at very center of the event; Biologists were teamed with Information Technology reseachers to tackle open biodiversity research questions based on EOL/TraitBank, and Biodiversity Heritage Library (BHL) data.

NoPlaceLikeHome, a project initiated and driven by Prof. Rob Stevenson, U Mass, Boston, aimed at exploring species - habitat associations. Significant contribution was received by the local collaborator Dr. Carl Nordman, NatureServe.

In this context ENVIRONMENTS was used to annotate in-house North and South America Bird (Aves) information such as ecology, habitat, migration descriptions and others. 

Heatmaps and tagclouds (see below) were generated to visualise the text mining results: species - EnvO term associations based on simple term counts.

The visualisation scripts have been developed as part of the SEQenv sister project to characterize microbial sample sequences, according to the environment from which they derive. 

Employed in a higher eukaryote context, the same tools can still support knowledge exploration e.g. by highlighting rare/frequent habitats, species habitat breadth, and intra-taxon environment association differences.

An even user-friendlier, interactive version of the graphicsis under way in collaboration with Dr. Umer Ijaz, Uni. of Glasgow

The image shown below is a compilation of the project outputs by Cyndy Parr, as found in the EOL Blog (among other reports from the NESCent EOL-BHL Research Sprint and EOL News). Quoting Cyndy's to-the-point legend: "Species are on the X axis and the Environment Ontology (EnvO) habitat term associations on the Y axis, with the redness (or size in the inset Wordle) based on simple term counts."  







Tuesday, October 29, 2013

September – October 2013: ENVIRONMENTS-EOL Outreach (BioCreative IV, TDWG 2013), E600 Housekeeping


Outreach activities have been the main focal point so far in Autumn 2013.

ENVIRONMENTS, ENVIRONMENTS-EOL, and the sister project SPECIES have been presented at an invited talk at the BioCreative IV workshop (7 - 9 October, Washington DC, US) as part of a DOE-funded Discussion Panel on Metagenomics.

Bridging the metagenomics and text mining communities e.g. by employing text mining techniques to support standards-compliant sequence metadata annotation was one of the main discussion points.
The Biocreative IV workshop proceedings including opinions on the previous point are available here (see Volume 1, pages 279-291).

On behalf of the ENVIRONMENTS-EOL team a big thank you to the BioCreative organizers.

At the time of writing, the Biodiversity Information Standards Conference (TDWG 2013, 28 Oct - 1 Nov, Firenze), is on-going.

ENVIRONMENTS-EOL will be be presented this Friday (1st Nov, 11:20) in the "Interoperability with genomic and ecological semantics" session of the Semantics for Biodiversity Symposium of TDWG2013 (Travel made possible thanks to EOL Rubenstein Fellows Program's funding).

In parallel and while the benchmarking algorithms are being prepared, the ENVIRONMENTS-600 (E600) corpus returned by the curators (see August's post) underwent housekeeping processing e.g. by removing any errors that had been introduced during the manual curation such as missing tabs in the annotation items, flag misspellings and others.

A mountain range (ENVO:00000080) as seen on board a flight from M√ľnich, Germany to Florence, Italy to attend TDWG2013. Could it be the Dolomite mountain range?


Saturday, September 14, 2013

August 2013: The E600 curation month

Amid July – August high temperatures for some of the team members, visits in associate labs for some others, and as a side-activity to normal lab/office work for the rest, the most tedious and time-consuming part of this project has now been completed.

Environments-600 (E600), a corpus comprising 600 EOL Taxa pages was evenly and randomly distributed among the 6 curators (4 graduate students, 2 postdocs, see June’s post).

To maximize environment type coverage the 600 EOL documents were species pages randomly picked from the following eight taxonomic taxa: Actinopterygii, Annelida, Arthropoda, Aves, Chlorophyta, Mammalia, Mollusca, Streptophyta. These are taxa either associated with different environments to each other, or known to exist in a diverse range of environments.

Each curator had 45 days to annotate 120 documents (ie. their part of the corpus: 600/6 = 100 documents each, plus 20 documents (ie. 20% of 100) that are common with other curators. The ‘20% overlap’ is an important part of the curation process. It supports the calculation of the Inter-annotator agreement (IAA, based on pairwise calculations of the Cohen's kappa coefficient.

Each curator had access to his/her own documents only. No information on the shared documents had been disclosed.

All curators were instructed to evaluate all document substrings and map the recognized environment descriptors to the corresponding EnvO terms.

Reflecting on the EnvO, envo-basic.obo, version-date: 14th June 2013, such environment descriptors included: habitats, biomes, enviromental features, conditions and materials (EnvO high level terms:  00002036, 00000428, 00002297, 01000203, 00010483 respectively)

All recognized mentions should be listed (including repetitions) in the order of appearance in text. To facilitate EnvO term search and ontology browsing OBO-Edit has been employed.

When an environment descriptor could refer to more than one EnvO terms multiple mappings were allowed (e.g. mapping “forest” to ENVO:00000111, “forest” (environmental feature), and  01000174, “forest biome”).

In the case of “nested” environment descriptors, a “left-longest most”-like matching approach applied. If for example “sandy sediment” is met in text, it will be mapped to ENVO: 01000118, “sandy sediment” (and not to the nested terms: sand, sediment).

During the curation a range of special cases were encountered. Cases like misspellings, EnvO term missing synonyms and enumerations were indicated as such. Environment descriptors that did not correspond to an existing EnvO term were also marked as such.

Finally, when environment descriptive terms where part of geographical locations and/or common taxon names (e.g. Steppe Eagle, Aquila nipalensis, shown in the Figure) were flagged as such to allow for downstream analysis.

Calculating the IAA, merging the annotated document in a single corpus are now ongoing, paving the ground for the ENVIRONMENT’s accuracy benchmark. Stay tuned!



Steppe Eagle, Aquila nipalensis, a common species name including a reference to an environment. Such cases occurred during the curation have been flagged for follow-up analysis (Image License: CC BY NC SA, © Tarique Sani, Source: Flickr: EOL Images) 

Friday, August 9, 2013

July 2013: First Deliverables: Tagger, Dictionary, Stopword-list: v1.0 Ready!

July 2013 has been a highly active month. 

A visit of  Dr. Lars Juhl Jensen in HCMR (Hellenic Center for Marine Research), Crete followed up on last April’s ENVIRONMENTS software developments (see post).

The main focus was on updating the dictionary and the stopword-list according to the information contained in a recent Environmental Ontology version (envo-basic.obo, date: 14 June 2013)

The Environmental Ontology updates including an improved coverage of terrestrial biomes (see EnvO News post) were the main reason for such an update.

As a result, the v1.0 ENVIRONMENTS tagger is now ready and has been delivered to EOL (including the latest dictionary of environment descriptive terms and the relevant stopword-list). All these software components are open source and will be made available at due time.

An annotation of all EOL-Taxon pages using the v1.0 tagger, along with a precision analysis of the different EOL page section annotation have been completed.

The gold standard corpus curation and the analysis of ENVIRONMENTS’ accuracy based on that corpus are now the main focus. 600 EOL species pages (from eight taxonomic taxa: Actinopterygii, Annelida, Arthropoda, Aves, Chlorophyta, Mammalia, Mollusca, Streptophyta – to maximize environment diversity) have now been shared among the curators and the manual annotation is ongoing.

At the mean time brief holiday opportunities arise :) (Picture taken at Ancient Falasarna, Chania, Crete, Early August 2013, CC BY-NC-SA)

Thursday, July 4, 2013

June 2013: The “dry-run” curation month

A gold standard corpus generation comprises steps such as: document collection/selection, manual document annotation, annotation result collection and statistical analysis.

The first and last steps can be computationally assisted and partially automated. However, this is not the case for the manual document annotation. Also called “curation”, the manual document annotation comprises the manual scanning of the document text to identify environment descriptive terms and map them to unique identifiers according to a community resource (the Environment Ontology (EnvO) in this case).

The tediousness and time-demands of such process call for collaborative effort. Aa international group of six researchers: Lucia Fanini, Sarah Faulwetter, Evangelos Pafilis, Christina Pavloudi, Julia Schnetzer, Katerina Vasileiadou (in alphabetical order) have undertaken this task. 

Coming from a diverse range of scientific background (such as ecology, computational biology, molecular biology, and systematic) they represent different mindsets upon scanning pieces of text, in a way representing different EOL readers.

Such pluralism is a desired feature for the corpus curation, however a common understanding among team members has to be established.

This was one of the main aims of the test curation (“dry run”) that took place during June 2013. A small set of documents (Text sections from EOL species pages, see post) were delivered to all curators. Upon manually annotating these documents curators  collected as many questions as possible around unclear and/or problematic annotation cases. Some examples of the latter are: terms and/or synonyms missing from EnvO, words that could be mapped to multiple EnvO terms, location names, nested environment descriptive terms.

A strategy employing a set of flags to indicate such cases is now in place. The previously generated the curation guideline document (see post) has  been updated accordingly and the production-level curation may now start.

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text @ PLOS ONE

The sister projects of SPECIES and ORGANISMS now published at PLOS ONE, part of the PLOS Text Mining Collection.

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. (2013) PLoS ONE 8(6): e65390. doi:10.1371/journal.pone.0065390
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0065390

The knowledge, skills and know-how gained through this work paved the ground for ENVIRONMENTS.

A big thank you to the team, Evangelos

Monday, June 3, 2013

May 2013: gearing up the corpus curation, mining names and synonyms from EOL content, following closing EnvO developments

A “beach sand” (ENVO:00002138) picture taken at the island of Chrisi, a Natura 2000 site south-east of Crete, Greece. “Coarse beach sand” (ENVO:00002148) can be observed along with shells forming a “biogenous sediment” (ENVO:01000082); a unique feature of this island. Besides the “Coarse beach sand” are all types of sand included in the Environment Ontology? Can the Environments-EOL project assist in proposing terms, names and synonyms? (Image: CC BY-NC-SA)

The Environments-EOL project is nearing its main stages (corpus creation, tagger  bench-marking, EOL annotation and taxa characterization, to take place in Summer 2013). To this end a range of preparatory tasks are being/have been conducted.

May 2013 has seen a “dry-run” curation being setup. A small set of document is being used for a trial curation (ongoing). The manual and lengthy nature of a corpus generation dictates tests take place before the main body of work commences. Via such a “dry-run” curators are getting familiarized with the Environment Ontology as well as with relevant browsing and searching tools. Additionally, questions are being raised and discussions invoked on the exact context of terms to be annotated by the Environments-EOL project.

In parallel: early tests showed that the manual addition of synonyms in the dictionary (see “Dictionary Generation in previous post”) could improve the tagger performance. To facilitate such task specialized EOL sections (e.g. Habitat) have been analyzed (counting word frequency in non-tagged text segments).  A priority list of terms to be considered was derived. After manual inspection environment related words have been mapped to EnvO terms and can now be added in the dictionary. The EOL records involved in this training step have been excluded from the corpus generation (and subsequently the software evaluation).

Last but not least: Environments-EOL is a project tightly bound to the Environment Ontology community resource. Highlighting this connection as well the projects’ dynamic nature: a thank you for the EnvO team’s prompt and timely response in updating the "terrestrial biome" hierarchy, comprising now more compact and fine grained terms (see EnvO News Post)