biochem4j: Integrated and extensible biochemical knowledge through graph databases Article Swipe
Neil Swainston
,
Riza Batista-Navarro
,
Pablo Carbonell
,
Paul D. Dobson
,
Mark S. Dunstan
,
Adrian J. Jervis
,
María Vinaixa
,
Alan Williams
,
Sophia Ananiadou
,
Jean‐Loup Faulon
,
Pedro Mendes
,
Douglas B. Kell
,
Nigel S. Scrutton
,
Rainer Breitling
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0179130
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0179130
Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.
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- Type
- article
- Language
- en
- Landing Page
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- https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0179130&type=printable
- OA Status
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- Cited By
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- References
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- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2736196485Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1371/journal.pone.0179130Digital Object Identifier
- Title
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biochem4j: Integrated and extensible biochemical knowledge through graph databasesWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2017Year of publication
- Publication date
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2017-07-14Full publication date if available
- Authors
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Neil Swainston, Riza Batista-Navarro, Pablo Carbonell, Paul D. Dobson, Mark S. Dunstan, Adrian J. Jervis, María Vinaixa, Alan Williams, Sophia Ananiadou, Jean‐Loup Faulon, Pedro Mendes, Douglas B. Kell, Nigel S. Scrutton, Rainer BreitlingList of authors in order
- Landing page
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https://doi.org/10.1371/journal.pone.0179130Publisher landing page
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0179130&type=printableDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0179130&type=printableDirect OA link when available
- Concepts
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UniProt, Workflow, Computer science, Biological database, Database, World Wide Web, Data science, Biological data, Web resource, Graph database, Web service, Data integration, Graph, Bioinformatics, Biology, Theoretical computer science, Gene, BiochemistryTop concepts (fields/topics) attached by OpenAlex
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44Total citation count in OpenAlex
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2025: 1, 2024: 8, 2023: 4, 2022: 8, 2021: 3Per-year citation counts (last 5 years)
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55Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| primary_location.pdf_url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0179130&type=printable |
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| primary_location.raw_source_name | PLOS ONE |
| primary_location.landing_page_url | https://doi.org/10.1371/journal.pone.0179130 |
| publication_date | 2017-07-14 |
| publication_year | 2017 |
| referenced_works | https://openalex.org/W1935434993, https://openalex.org/W2159482845, https://openalex.org/W2142678031, https://openalex.org/W2464278521, https://openalex.org/W2013434113, https://openalex.org/W2038733937, https://openalex.org/W2605068739, https://openalex.org/W2166138679, https://openalex.org/W1952732684, https://openalex.org/W2140445011, https://openalex.org/W6736874787, https://openalex.org/W2221682991, https://openalex.org/W2123604001, https://openalex.org/W2560036845, https://openalex.org/W2564769250, https://openalex.org/W2045686929, https://openalex.org/W2202347610, https://openalex.org/W2158784643, https://openalex.org/W4237335579, https://openalex.org/W2093666160, https://openalex.org/W2015809202, https://openalex.org/W2077513513, https://openalex.org/W2170146596, https://openalex.org/W2053385401, https://openalex.org/W1508604947, https://openalex.org/W2114688451, https://openalex.org/W2009453329, https://openalex.org/W7075630220, https://openalex.org/W1989962769, https://openalex.org/W2149948001, https://openalex.org/W1985512202, https://openalex.org/W2092448217, https://openalex.org/W2160719116, https://openalex.org/W2024038403, https://openalex.org/W2110679449, https://openalex.org/W1989263028, https://openalex.org/W2150908245, https://openalex.org/W2149741353, https://openalex.org/W2418056440, https://openalex.org/W2140181854, https://openalex.org/W2292734588, https://openalex.org/W2146744007, https://openalex.org/W115574301, https://openalex.org/W2128763542, https://openalex.org/W2078355959, https://openalex.org/W1910839236, https://openalex.org/W1969389753, https://openalex.org/W2611196248, https://openalex.org/W2806394571, https://openalex.org/W2544136853, https://openalex.org/W1989277387, https://openalex.org/W1604281503, https://openalex.org/W2786122698, https://openalex.org/W4233659707, https://openalex.org/W4252180373 |
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