Evangelos Profile Picture

Evangelos Pafilis is a Research Fellow at the Hellenic Center for Marine Research in Crete, Greece. He is involved in the LifeWatch Greece project (following up on a MARBIGEN EU REGPOT Experienced Researcher position).

Coming from a background in data integration and literature mining in the biomedical domain, he is exploring how such techniques could also serve other biological research fields. The overall aim is to support answering questions that span the whole spectrum of biological organization: from genes all the way up to ecosystems.

His present focus is in the recognition of organism names and environment descriptors mentioned in text. Bioinformatics analyses, information visualization, network-based analysis and data mining of large/global scale resources, such as GenBank, PubMed, the Encyclopedia of Life, and the Biodiversity Heritage Library, are the means to this end.

News

Jun 2015: Talk Given: Associating Organisms with their Environment [PDF] at the EMODnet WG2/WG4-EUBON WP3 Joined Session (HCMR, Crete, Greece)

May 2015: Talk Given: Text Mining and Environmental Metadata Suggestion [PDF] at the GSC 17 - Genomic Standards Consortium Workshop (DOE JGI, Walnut Creek, CA, US)

Jan 2015: Published: ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life, Pafilis E, et al. Bioinformatics, 2015, doi:10.1093/bioinformatics/btv045

Dec 2014: Lecture Given: Text Mining and Environmental Metadata Suggestion [PDF] at the "ENA/EMG Sample Record Annotation Workshop (Jamboree)" (EBI, Hinxton, UK) Many thanks to Guy, Petra, et al. for the funding and the hosting

Oct 2014: Talk Given: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life [PDF] at TDWG 2014, the annual conference of the Biodiversity Information Standards community (Jönköping, Sweden) Thanks to funding from LifeWatch Greece

Sept 2014: Organized: Workshop-Hackathon SEQenv III: From Signals to Environmentally Tagged Sequences III, focus on Vizualisation (HCMR Crete, Greece, thanks to funding from the EU COST Action ES1103 and support from LifeWatch - Greece )

Jul 2014: Published: BioTextQuest+: A knowledge integration platform for literature mining and concept discovery, Papanikolaou N, Pavlopoulos GA, et al. Bioinformatics, 2014, 30(22):3249Ğ3256

Jun 2014: Lecture Given: "Metadata and Standardization, OSD - a Powerful Example" at the MicroB3 Summer School: From sampling to analyzing microbial diversity & function (HCMR Crete, Greece)

May/Jun 2014: Co-organized: MicroB3 Summer School: From sampling to analyzing microbial diversity & function (HCMR Crete, Greece)

Mar/Apr 2014: Talk Given: "ENVIRONMENTS: EnvO term identification in text" at GSC 16, The 16th workshop of the Genomic Standards Consortium (Oxford, UK) Thanks to funding from LifeWatch Greece

Mar 2014: Published: Commentary: The Founding Charter of the Genomic Observatories Network Davies N, Field D, Amaral-Zettler Let al. (2014) GigaScience, 3:2 doi:10.1186/2047-217X-3-2

Feb 2014: Participated: NESCent-EOL-BHL Research Sprint (Durham, NC, US) Check out some output-describing blog posts at: EOL, Environments-EOL

Jan 2014: Published: Polytraits: A database on biological traits of marine polychaetes Faulwetter S et al. (2014) Biodiversity Data Journal, 2: e1024. doi: 10.3897/BDJ.2.e1024

Dec 2013: Talk Given: SEQenv: annotating sequences with environments in EU COST Action ES1103 workshop: Bioinformatics meets microbial ecology (BMME) (Prague, Czech Republic)

Nov 2013: Participated: EU COST Action ES1103: Microbial ecology & the earth system Management Committee Meeting (Bergen, Norway)

Oct/Nov 2013: Talk Given: Identification of Environment Ontology terms in Text and Annotation of Biodiversity and Genomics Information at TDWG2013 - Semantics for Biodiversity Symposium - Session 3: "Interoperability with genomic and ecological semantics" (Florence, Italy)

Oct 2013: Published: Beach parties: a case study on recreational human use of the beach and its effects on mobile arthropod fauna. Fanini L, Zampicinini G, Pafilis E. (2013) Ethology Ecology & Evolution doi:10.1080/03949370.2013.821674

Oct 2013: Plenary Talk: SPECIES and ENVIRONMENTS Taxonomic name and environment descriptive term identification in text at Biocreative IV (Washington DC, US) as part of a DOE-funded Discussion Panel on Metagenomics. A big thank you to the organizers. Find out more on the Workshop Proceedings

Sept 2013: Accepted: OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction Pafilis E, Pavlopoulos GA, Satagopam V, Papanikolaou N, Horn H, et al. 13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE13) November 2013, Chania, Greece in press

Jul 2013: Poster: OnTheFly 2.0: Automated Annotation of Scientific Documents at ISMB/ECCB 2013 (Berlin, Germany)

Jul 2013: Attended: LifeWatch Lifewatch Inter-ministerial meeting (Sevilla, Spain)

Jul 2013: Co-Organized: Bluehackathon 2013 workshop (HCMR Crete, Greece)

Jun 2013: Published: 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.

Jun 2013: Organized: Workshop-Hackathon "From Signals to Environmentally Tagged Sequences II" (HCMR Crete, Greece, thanks to funding from the: EU COST Action ES1103)

Apr 2013: Published: A decadal view of biodiversity informatics: challenges and priorities. Hardisty A, Roberts D, Biodiversity Informatics Community BMC Ecol. 2013 Apr 15;13:16. (contributing author)

Apr 2013: Poster (~15MB) and Talk Given: ENVIRONMENTS: Identification of Environment Descriptive Terms in Text at GSC 15 - Genomic Standards Consortium Workshop (Washington DC, US)

Apr 2013: Attended: GSC 15 - Genomic Standards Consortium Workshop (Washington DC, US)

Apr 2013: Attended: Genomic Observatories Network second meeting at GSC 15 (Washington DC, US)

Mar 2013: Oficial Start: ENVIRONMENTS-EOL project (funded by Encyclopedia of Life - Rubenstein 2013 Fellowship ). Monthly updates in this blog

Feb 2013: Talk Given: "Mining the Scientific Literature for Biodiversity Knowledge" at the first MARBIGEN Evaluation Committee Meeting (Heraklio, Greece)

Jan 2013: Awarded: Encyclopedia of Life - Rubenstein 2013 Fellowship for the ENVIRONMENTS project (Project Blog available here, software website availabe here)

Dec 2012: Talk Given: "SPECIES and ENVIRONMENTS: taxonomic name and environment descriptive term identification in text" at HCHMR-IMBBC Seminars (Heraklio, Greece)

Oct 2012: Talk Given: "SPECIES: Organism Name Identification in the Scientific Literature" at HSCBB 2012 (Heraklio, Greece)

Sept 2012: Organized: Workshop-Hackathon "From Signals to Environmentally Tagged Sequences" (HCMR Crete, Greece, thanks to funding from the: EU COST Action ES1103)

Sept 2012: Attended: GSC 14 - Genomic Standards Consortium Workshop (Oxford, UK)

Sept 2012: Attended: Genomic Observatories Network meeting at GSC 14 (Oxford, UK)

Sept 2012: Attended: Workshop-Hackathon "Hackathon on Field Information Management Systems (FIMS) with a focus on interoperability" (Oxford, UK, thanks to funding from the: EU COST Action ES1103)

Jun 2012: Attended: EU-US Training in Marine Bioinformatics (Bremen, Germany, thanks to funding from the EU-US Task Force Bio Triangle Project)

Apr 2012: Talk Given: "Connecting Scientific Data and Documents incl. HCMR Text Mining Efforts" in ViBRANT Technical Workshop (Sofia, Bulgaria)

Mar 2012: Attended: EMBRC International Workshop on Marine E-Infrastructure (EMBL, Heidelberg, Germany)

Feb 2012: Course Given: A Short Introduction to Unix for Bioinformatics as part of " Introductory course to the Principles of Coalescent Theory and Applications" (HCMR Crete)

Feb 2012: Attended: MicroB3 Kick-off meeting (Bremen, Germany)

Jan 2012: Talk Given: "HCMR efforts in connecting the two silos: scientific data and documents" in Euromarine Workshop on "Linking Scientific Data and Journal Publications" (Bremen, Germany)

Dec 2011: Attended: "Microbial Diversity, Genomics and Metagenomics" Workshop (HCMR Crete)

Nov 2011: Attended: Introduction to Systems Biology (HCMR Crete)

Nov 2011: Awarded: EMBO Short Term Fellowship (356-2011) to visit the Novo Nordisk Foundation Center for Protein Research in Copenhagen, Denmark (Nov - Dec 2011)

Nov 2011: Published: Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT. Arvanitidis, C, Faulwetter S, Chatzigeorgiou G, Penev L, Bankí O, Dailianis T, Pafilis E, Kouratoras M, Chatzinikolaou E, Fanini L et al. (2011). Zookeys, 2011, 150:211-219.

Oct 2011: Published: BioTextQuest: a web-based biomedical text mining suite for concept discovery. Papanikolaou, N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ. (2011). Bioinformatics, 2011, 27(23):3327-3328

Oct 2011: Poster and Talk Given: "OnTheFly 2.0: A Service to automatically annotate files and extract biological information" at HSCBB 2011, Patras, Greece

Sept 2011: Book Chapter Submitted: "Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge" Pafilis, E, Horn H, Brown NP

July 2011: Field Trip: "Lagoon Polychaete worm sampling" (Amvrakikos, Greece)

June 2011: Course Given: "Introduction to Programming Using Python" (18hrs, HCMR Crete)

May 2011: Field Trip: "Lagoon Polychaete worm sampling" (Amvrakikos, Greece)

The ENVIRONMENTS-EOL Project

1st Prize Award

Reflect Team is the winner of the Elsevier Grand Challenge!


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