Closing the gap between formats for storing layout information in systems biology

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F20%3A10421749" target="_blank" >RIV/00216208:11320/20:10421749 - isvavai.cz</a>

Výsledek na webu

<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=lnTHrjPNpl" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=lnTHrjPNpl</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bib/bbz067" target="_blank" >10.1093/bib/bbz067</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Closing the gap between formats for storing layout information in systems biology

Popis výsledku v původním jazyce

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.

Název v anglickém jazyce

Closing the gap between formats for storing layout information in systems biology

Popis výsledku anglicky

The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2020

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Briefings in Bioinformatics

ISSN

1467-5463

e-ISSN

—

Svazek periodika

21

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

12

Strana od-do

1249-1260

Kód UT WoS článku

000576139100010

EID výsledku v databázi Scopus

2-s2.0-85088265787