Scientific Databases and Visualisation

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SEEK ID: https://publications.h-its.org/projects/3

Public web page: https://sdbv.h-its.org

Organisms: No Organisms specified

HITS Publication SEEK PALs: No PALs for this Project

Project created: 6th Oct 2017

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Dorotea Dudas

Projects: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

Sucheta Ghosh

Projects: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

https://orcid.org/0000-0002-2896-4552

Martin Golebiewski

Projects: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

https://orcid.org/0000-0002-8683-7084

Yachee Gupta

Projects: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

Xiaoming Hu

Projects: Scientific Databases and Visualisation, Computational Molecular Evolution, Physics of Stellar Objects, Natural Language Processing, Molecular and Cellular Modeling, Molecular Biomechanics, Astroinformatics, Groups and Geometry, Playground, Computational Carbon Chemistry, Data Mining and Uncertainty Quantification, Computational Statistics

Institutions: Heidelberg Institute for Theoretical Studies, Heidelberg University

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Heidelberg Institute for Theoretical Studies

Country: Germany

City: Heidelberg

Web page: https://www.h-its.org

Heidelberg University

Country: Germany

City: Heidelberg

Web page: http://www.uni-heidelberg.de/index_e.html

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

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Created: 27th Nov 2017 at 15:07

Figure_4

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Created: 27th Nov 2017 at 15:05

Figure_3

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Created: 27th Nov 2017 at 15:05

Figure_2

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Created: 27th Nov 2017 at 15:04

Figure_1

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Created: 27th Nov 2017 at 15:04

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A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Scientific Databases and Visualisation

Abstract (Expand)

Abstract The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host …

Authors: Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, Marc E. Gillespie, Akira Funahashi, Marcio Luis Acencio, Ahmed Hemedan, Michael Aichem, Karsten Klein, Tobias Czauderna, Felicia Burtscher, Takahiro G. Yamada, Yusuke Hiki, Noriko F. Hiroi, Finterly Hu, Nhung Pham, Friederike Ehrhart, Egon L. Willighagen, Alberto Valdeolivas, Aurelien Dugourd, Francesco Messina, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Sylvain Soliman, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Aurélien Naldi, Tomáš Helikar, Vidisha Singh, Marco Fariñas Fernández, Viviam Bermudez, Eirini Tsirvouli, Arnau Montagud, Vincent Noël, Miguel Ponce de Leon, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Augustin Luna, Janet Pinero, Laura I. Furlong, Irina Balaur, Adrien Rougny, Yohan Jarosz, Rupert W. Overall, Robert Phair, Livia Perfetto, Lisa Matthews, Devasahayam Arokia Balaya Rex, Marija Orlic-Milacic, Monraz Gomez Luis Cristobal, Bertrand De Meulder, Jean Marie Ravel, Bijay Jassal, Venkata Satagopam, Guanming Wu, Martin Golebiewski, Piotr Gawron, Laurence Calzone, Jacques S. Beckmann, Chris T. Evelo, Peter D’Eustachio, Falk Schreiber, Julio Saez-Rodriguez, Joaquin Dopazo, Martin Kuiper, Alfonso Valencia, Olaf Wolkenhauer, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider

Date Published: 19th Dec 2022

Publication Type: Misc

DOI: 10.1101/2022.12.17.520865

Citation: biorxiv;2022.12.17.520865v1,[Preprint]

Created: 23rd Jan 2023 at 10:57, Last updated: 23rd Jan 2023 at 10:59

ISO 20691:2022 Biotechnology — Requirements for data formatting and description in the life sciences

Scientific Databases and Visualisation

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This document specifies requirements for the consistent formatting and documentation of data and corresponding metadata (i.e. data describing the data and its context) in the life sciences, including …

Author: Martin Golebiewski

Date Published: 4th Nov 2022

Publication Type: Misc

Citation:

Created: 23rd Jan 2023 at 12:13

More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics

Scientific Databases and Visualisation

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SABIO-RK represents a repository for structured, curated, and annotated data on reactions and their kinetics. The data are manually extracted from the scientific literature and stored in a relational …

Author: Andreas Weidemann, Dorotea Dudas, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 1st Aug 2022

Publication Type: Journal

DOI: 10.7490/f1000research.1119079.1

Citation:

Created: 8th Feb 2023 at 11:44

Towards Effortless Navigation of Scientific-Literature Screen Reading for Biocuration

Scientific Databases and Visualisation

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Background: the exponential growth of bio-literature has stirred the need for digitization of the biocuration processes. In this context, it is observed that screen reading of electronic documents paces … up the whole process and also induces collaborative annotation in biocuration1. The usability experiences of screen-reading in the biocuration context are still an under-explored area. In other contexts, studies found that cumbersome navigational issues hamper intensive reading. It results in lower reading speeds (and thus, slower understanding) and fatigue when reading for an extended period, which leads to an increment in curation cost. On the other side, studies found that improvement of the organization of the electronic document can facilitate faster reading and understanding2. Objective: To our knowledge, this is the first and preliminary usability experience study to observe the effect of the navigation through the electronic document structure for the biocuration task. Method: We conduct a curation task with the five curators for eighty papers in front of an eye tracker. We collect the level of difficulty on the Likert scale from the participants and their preferences for document structure. We explore different features for our statistical and correlation analysis: errors made by curators (checked by the other two expert curators), efforts made by the curators measured using an eye tracker. We used several eye tracker features, namely, time spent for reading, time spent for navigation, top-down reading time, bottom-up reading time, reading speed, fixation duration at different parts of the document, and pupillary responses. Result: We find that the concurrent rhetorical and document structure facilitates fast reading. In this case, the navigational effort comes down significantly, especially for the experienced curators. It implies from this study that concurrent rhetorical structure3 and document layout facilitate reading for digital biocuration. While in these experiment we did not see direct signs for explicit structural weaknesses of the paper, we are planning to investigate the impact of structural changes on the readiblity of papers. The key difficulty in this work is obtaining sufficiently large group of test persons able to read complex scientific publications. 1 W3C Web Annotation Working Group. (2022, April 4). To enable a conversation over the world’s knowledge: Hypothesis Mission. https://web.hypothes.is 2 Hornbæk, K., & Frøkjær, E. (2003). Reading patterns and usability in visualizations of electronic documents. ACM Transactions on Computer-Human Interaction (TOCHI), 10(2), 119-149. 3 Teufel, S., Siddharthan, A., & Batchelor, C. (2009, August). Towards domain-independent argumentative zoning: Evidence from chemistry and computational linguistics. In Proceedings of the 2009 conference on empirical methods in natural language processing (pp. 1493-1502).

Author: Sucheta Ghosh, W Mueller, U Wittig, M. Rey

Date Published: 5th May 2022

Publication Type: InProceedings

DOI: 10.5281/zenodo.7525550

Citation:

Created: 11th Jan 2023 at 14:37

The Effect of an Additional Structured Methods Presentation on Decision-Makers' Reading Time and Opinions on the Helpfulness of the Methods in a Quantitative Report: Nonrandomized Trial.

Scientific Databases and Visualisation

Abstract (Expand)

BACKGROUND: Although decision-makers in health care settings need to read and understand the validity of quantitative reports, they do not always carefully read information on research methods. Presenting …

Authors: J. Koetsenruijter, P. Wronski, S. Ghosh, W. Muller, M. Wensing

Date Published: 12th Apr 2022

Publication Type: Journal

PubMed ID: 35412464

Citation: JMIR Med Inform. 2022 Apr 12;10(4):e29813. doi: 10.2196/29813.

Created: 11th Jan 2023 at 13:59

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LiSyM's Development Pipeline

Scientific Databases and Visualisation

Presentation at PALS meeting, Huenfeld 2-3.5.17

Creator: Hadas Leonov

Submitter: Hadas Leonov

Created: 10th Nov 2017 at 11:13

Scientific Seminar 30.1.17

Scientific Databases and Visualisation

Joint Presentation of NMTrypI-related work with Joanna (this is only my part)

Creator: Hadas Leonov

Submitter: Hadas Leonov

Created: 10th Nov 2017 at 11:11

HITS Lab Meeting 9..1.17

Scientific Databases and Visualisation

Presentation of NMTrypI features at HITS

Creator: Hadas Leonov

Submitter: Hadas Leonov

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Created: 10th Nov 2017 at 11:09

Drug Discovery Enhancing Systems

Scientific Databases and Visualisation

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Poster for conference "Human Bioinformatics and Disease" Nov/16, Heidelberg

Creators: Hadas Leonov, Ulrike Wittig, Wolfgang Müller

Submitter: Hadas Leonov

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Created: 10th Nov 2017 at 11:02, Last updated: 10th Nov 2017 at 11:03

SABIO-RK Finding, Curating, and Publishing Data

Scientific Databases and Visualisation

No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Created: 8th Nov 2017 at 10:33

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8th ELIXIR All Hands meeting

The meeting brings together members of the ELIXIR community from across the ELIXIR Nodes, and collaborators from partner organisations, in order to review ELIXIR’s achievements and activities so far and discuss plans for the future.

Start Date: 7th Jun 2022

End Date: 10th Jun 2022

Event Website: https://elixir-europe.org/events/elixir-all-hands-2022

Country: Netherlands

City: Amsterdam

Created: 8th Feb 2023 at 11:56, Last updated: 8th Feb 2023 at 11:56

LiSyM PALS Meeting

No description specified

Start Date: 2nd May 2017

End Date: 3rd May 2017

Event Website: https://seek.lisym.org/events/1

Country: Germany

City: Huenfeld

Created: 10th Nov 2017 at 11:17, Last updated: 10th Nov 2017 at 11:19

Kinetics on the move: Workshop on Data for Computational Modeling

Motivation:

Do you work in the lab and always wonder what these bioinformaticians do with the data you generate? Would you like to use models to verify a hypothesis or test your experimental data? Then this workshop may be right for you.

The first day of the workshop focuses on data. We will celebrate the 10th anniversary of SABIO-RK with talks and practical training relating to the publication, curation, retrieval, and usage of kinetic data from SABIO-RK.The second day of the workshop focuses ...

Start Date: 30th May 2016

End Date: 31st May 2016

Event Website: https://www.h-its.org/sdbv-previous-events/kinetics-on-the-move-workshop/

Country: Germany

City: Heidelberg

Created: 8th Nov 2017 at 10:29

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