Málaga Workshop

Málaga Workshop

When 21 February, 2019 - This activity is over

The role of text mining in curation workflows

Short description:

At the Málaga workshop we will discuss how Text Mining can best be incorporated into curation workflows of scientific information together with the sharing of the results produced by this technology.

Local organiser(s):

María del Mar Roldán García

Agenda:

Workshop Organisers:

Martin Krallinger
Fabio Rinaldi
Marcio Luis Acencio
Martin Kuiper

21 of February:

Morning session:

09:00 – 09:10: Workshop – scope and aims (Martin Kuiper)
09:10 – 09:50: Session 1 – Gentle introduction to text mining and gene regulation (Chair: Astrid Lægrid)
- 09:10 – 09:30: Text-mining basics and how it can assist curation (Fabio Rinaldi)
- 09:30 – 09:50: Fundamentals of gene regulation and the GREEKC Working Group 2 (Sandra Orchard)
09:50 – 12:20: Session 2 – Curation needs in the 5 different areas of Working Group 2 (Chair: To be announced)
- 09:50 – 10:05: Protein level: transcription factors and co-factors (Ruth Lovering)
- 10:05 – 10:20: Non-coding RNA level: miRNAs and beyond (Simona Panni)
- 10:20 – 10:35: Genome level: Transcription Factor Binding Sites and regulatory elements (Colin Logie)
- 10:35 – 10:50: Interaction level: Dealing with Causality (Vasundra Touré)
10:50 – 11:20: Coffee break
11:20 – 11:50: Discussion: How can text mining meet these diverse and precise curation needs?
11:50 – 12:20: Initial considerations about the hackathon/jamboree session (Fabio Rinaldi / Martin Krallinger)
12:20 – 13:00: Keynote lecture – Title to be announced (Alfonso Valencia)
13:00 – 14:00: Lunch

Afternoon session:

14:00 – 16:00: Session 3 – Text mining solutions – what works and what does not (Chair: To be announced)
- 14:00 – 14:20: Text mining in the Wikipathways initiative (Susan Coort)
- 14:20 – 14:40: ExTRI: extraction of DbTF-TG interactions from abstracts (Fabio Curi Paixao)
- 14:40 – 15:00: The Dark Space Project (Pablo Porras)
- 15:00 – 15:20: LION LBD: a literature-based discovery system for cancer biology (Sampo Pyysalo)
- 15:20 – 15:40: How can the Visual Syntax Method (http://scicura.org/info.html) meet text mining?
- 15:40 – 16:00: Discussion: listing of questions and discussion topics for further discussion
16:00 – 16:30: Coffee break
16:30 – 17:30: Session 4 – Applicability of text mining for GREEKC objectives (Chairs: Fabio Rinaldi, Martin Krallinger and Martin Kuiper)
- 16:30 – 17:30: Open discussion on topics raised in Session 3:
  - What are the areas with low hanging fruit, what are the bottlenecks?
  - What uses are best addressed by what text mining pipeline?
  - Other
- 16:30 – 17:30: Introduction to the hackathon/jamboree tasks:
  - 16:30 – 17:00: Text mining pipeline hackathon (Fabio Rinaldi)
  - 17:00 – 17:30: Curation jamboree (Martin Krallinger)

Social Activities:

19:00: Guided tour around the city center (meeting point at Plaza de la Merced – Google Maps)
20:30: Dinner at “La Reserva del Olivo” – Google Maps

22 of February:

Morning session:

09:00 – 09:40: Keynote lecture – Using text mining in biomedical databases (Lars Juhl Jensen)
Plenary session:
- 09:45 – 13:00: Session 5 – Quality metrics and sharing of text mining (Chair: Pablo Porras)
- 09:45 – 10:00:Extracting microRNA-gene relations from biomedical literature using distant supervision (André Lamúrias)
- 10:00 – 10:15: Quality metrics for text mined data: Dark Space (Pablo Porras)
- 10:30 – 11:00: Discussion: how can we improve QM? Are there other handles we can use for confidence and trust?
- 11:00 – 11:30: Coffee break
- 11:30 – 11:50: Sharing the ExTRI resource via Biogateway (Martin Kuiper)
- 11:50 – 12:10: Configurable web-services for biomedical document annotation (Sergio Matos)
- 12:10 – 12:30: EuropePMC SciLite annotations (Xiao Yang)
- 12:30 – 13:00: Discussion: the future for sharing of gene regulation-related text mined data/provenance checking
Text mining hackathon breakout:
- 09:45 – 09:50: Getting ready (Fabio Rinaldi)
- 09:50 – 11:00: Hands-on session
- 11:00 – 11:30: Coffee break
- 11:30 – 13:00: Hands-on session (continued)
Curation jamboree breakout:
- 09:45 – 09:50: Getting ready (Martin Krallinger)
- 09:50 – 11:00: Hands-on session
- 11:00 – 11:30: Coffee break
- 11:30 – 13:00: Hands-on session (continued)
13:00 – 14:00: Lunch

Afternoon session:

14:00 – 16:00: Session 6 – Text mining integration into curation workflows (Chair: Fabio Rinaldi)
- 14:00 – 14:20: Assisted curation pipeline of RegulonDB (Carlos Méndez / Yalbi Balderas)
- 14:20 – 14:40: neXtA5: supporting biocuration activities at neXtProt (Pascale Gaudet)
- 14:40 – 15:00: To be announced
- 15:00 – 15:30: Discussion: how to build an effective text mining pipeline integrated to curation workflows in gene regulation?
15:30 – 16:00: Coffee break
16:00 – 17:30 – Session 7 – Closing remarks (Chairs: Fabio Rinaldi, Martin Krallinger and Martin Kuiper)
- 16:00 – 16:30: Hackathon and jamboree results (Martin Krallinger / Fabio Rinaldi)
- 16:30 – 17:00: New collaborations – the way forward
- 17:00 – 17:30: Next steps and action points

Social activities:

20:30: dinner at Restaurante Italiano La Tagliatella Muelle Uno – Google Maps

So far, the participants in this workshop are:

Alfonso Valencia (Barcelona Supercomputing Center)
Andre Lamurias (University of Lisboa)
Astrid Lægrid (Norwegian University of Science and Technology)
Aurelio Moya García (University of Málaga)
Belén Juanes Cortés (Spanish National Research Council)
Carlos Méndez (National Autonomous University of Mexico)
Colin Logie (Radboud Institute for Molecular Life Sciences)
Eduardo Andrés León (Spanish National Research Council)
Elena Díaz Santiago (University of Málaga)
Elena Rojano (University of Málaga)
Fabio Rinaldi (University of Zurich)
Fabio Curi Paixao (Barcelona Supercomputing Center)
Felipe Soares (Barcelona Supercomputing Center)
Fernando Moreno (University of Málaga)
Gonzalo Claros (University of Málaga)
Goran Nenadic (University of Manchester)
James Perkins (Biomedical Research Networking Centres)
José Córdoba Caballero (University of Málaga)
Joseph Bonello (University of Malta)
Juan A.G. Ranea (University of Málaga)
Lars Juhl Jensen (University of Copenhagen)
Livia Perfetto (European Bioinformatics Institute)
Lorena Aguilera Cobos (University of Málaga)
Luana Licata (University of Rome Tor Vergata)
Maciej Rybinski (University of Málaga)
María del Mar Roldán García (University of Málaga)
Martin Krallinger (Spanish National Cancer Research Center)
Martin Kuiper (Norwegian University of Science and Technology)
Miguel Ángel Medina Torres (University of Málaga)
Pablo Porras (European Bioinformatics Institute)
Pascale Gaudet (Swiss Institute of Bioinformatics)
Pedro Seoane Zonjuc (Biomedical Research Networking Centres)
Rune Nydal (Norwegian University of Science and Technology)
Ruth Lovering (London’s Global University)
Sampo Pyysalo (University of Turku)
Sandra Orchard (European Bioinformatics Institute)
Sandro Hurtado Requena (University of Málaga)
Sergio Matos (University of Aveiro)
Simona Panni (University of Calabria)
Stefan Schulz (Medical University of Graz)
Steven Vercruysse (Norwegian University of Science and Technology)
Susan Coort (University of Maastricht)
Tilia Ellendorff (University of Zurich)
Vasundra Touré (Norwegian University of Science and Technology)
Xiao Yang (European Bioinformatics Institute)
Yalbi Itzel Balderas Martínez (Mexican Council of Science and Technology)

If you are interested in attending the event please send a short motivation letter together with background information on your research interests to marcio.l.acencio@ntnu.no.

Accommodation:

The following link will take you to a Google Maps containing locations of the Venue, relevant bus stops, accommodation options and restaurants.

Some of the recommended accommodation options are:

Also, a dinner is organised on the 21st of February at the restaurant La Reserva del Olivo. The price will be 40 € per person. You can see the menu options here.