biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.

Markus J Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, Alexander Keller

Abstract read

In one paragraph

Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

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0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Markus J AnkenbrandDepartment of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany.

Niklas TerhoevenDepartment of Plant Physiology and Biophysics (Botany I), University of Würzburg, Würzburg, Germany; Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany.

Sonja HohlfeldDepartment of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany.

Frank FörsterCenter for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany; Department of Bioinformatics, University of Würzburg, Würzburg, Germany.

Alexander KellerDepartment of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component.

Indexed as

biojsbiom-formatecologymeta-barcodingmeta-genomicsparser

Identifiers

PMID28105307

DOI10.12688/f1000research.9618.2

PMCPMC5224677

What OpenQuestion holds

Textmetadata

LicenceCC BY

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.