Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis is a dataset published in Molecular Systems Biology (2021). On theSindex it has a DataRank of 4.4, placing it in the top 5% of the data-sharing corpus. It has been cited 380 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 29/100.
Ranks in the top 5% for downstream scientific impact
Linked data & code
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“The data are accessible via OmniPath’s web service ( https://omnipathdb.org/ )”— not found in the paper; verdict downgraded
The only identifier for the dataset is a web URL, which is not a persistent identifier scheme. [downgraded to 'no' — no verifiable quote from the paper]
RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit · RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier' · FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'
“The data are accessible via OmniPath’s web service ( https://omnipathdb.org/ )”— not found in the paper; verdict downgraded
The named host is the OmniPath web resource, a project website, not a curated repository listed in re3data/FAIRsharing. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]
RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed ( · NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived · NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten
“The data are accessible via OmniPath’s web service ( https://omnipathdb.org/ )”— not found in the paper; verdict downgraded
The dataset identifier appears only in the body text as a URL, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]
FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first- · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes · FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'
Advisory · not in the published score
“OmniPath is available via the Python package pypath ( https://github.com/saezlab/pypath ), the web resource ( https://omnipathdb.org ), the R/Bioconductor package OmnipathR ( https://saezlab.github.io/OmnipathR ), the omnipath Python client ( https://github.com/saezlab/omnipath ), and the OmniPath Cytoscape plug‐in (Ceccarelli et al, 2019).”— not found in the paper; verdict downgraded
The statement points to a web resource and code repositories, not to a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]
Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li · Springer Nature research data policy — Data Availability Statements: standard statement templat · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes
“The network database part covers four major domains of molecular signaling: (i) protein–protein interactions (PPI), (ii) transcriptional regulation of protein‐coding genes, (iii) miRNA–mRNA interactions, and (iv) transcriptional regulation of miRNA genes (TF‐miRNA).”
The dataset content is described in running prose, not in an itemised inventory. [majority verdict 'partial' (3/4 passes agreed)]
RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential) · FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability' · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'
“OmniPath is available via the Python package pypath ( https://github.com/saezlab/pypath ), the web resource ( https://omnipathdb.org ), the R/Bioconductor package OmnipathR ( https://saezlab.github.io/OmnipathR ), the omnipath Python client ( https://github.com/saezlab/omnipath ), and the OmniPath Cytoscape plug‐in (Ceccarelli et al, 2019).”— not found in the paper; verdict downgraded
The text gives multiple routes to the data with no stated precondition of embargo, registration, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 passes agreed)]
RDA-A1.1-01D — 'Data is accessible through a free access protocol' · FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'
Advisory · not in the published score
“The data are accessible via OmniPath’s web service ( https://omnipathdb.org/ )”— not found in the paper; verdict downgraded
The paper describes the action of accessing the data via a web service but does not label the access level with a standard term like 'open access'. [downgraded to 'no' — no verifiable quote from the paper]
FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · RDA-A1-01M — metadata contains information to enable the user to get access to the data · COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl
The data are not sensitive or human-subject, so no gatekeeper is named.
NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee · RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and · NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse
No sentence addresses when the data become available or how long they persist.
NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines · NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy' · RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'
“pypath is able to export the network and the enzyme–PTM databases in BEL (Biological Expression Language) format”
BEL is an open community-standard format named for the data.
FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co · RDA-R1.3-02D — data is expressed in a machine-understandable community standard · RDA-I1-01D — data uses a knowledge representation expressed in a standardised format
Advisory · not in the published score
“we built Boolean expressions from Gene Ontology terms to define the same categories.”
The paper uses Gene Ontology, a community standard ontology, to define categories.
RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential) · RDA-R1.3-01D — 'Data complies with a community standard' · RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'
“We applied our OmniPath‐based version of NicheNet analysis on RNA‐Seq data of a human lung cell line, Calu3 ( GSE147507 )”— not found in the paper; verdict downgraded
The paper provides a GEO accession (GSE147507) for a dataset used in the case study, which is a resource other than the paper's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]
RDA-I3-01M — '(meta)data include references to other (meta)data' · RDA-I3-03M — 'metadata includes qualified references to other metadata' · FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'
“All data in OmniPath carry the licenses of the original resources (Dataset EV12)”— not found in the paper; verdict downgraded
The data do not have a standard open license; they carry the licenses of the original resources, which is a named terms document but not a single open license. [downgraded to 'no' — no verifiable quote from the paper]
RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu · RDA-R1.1-02M — 'Metadata refers to a standard reuse licence' · RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'
No version token or date is given for the dataset itself; the software version is for the tool, not the data.
DataCite Metadata Schema 4.6 — the 'Version' property · RDA-R1.2-01M — provenance information (which version was used is provenance) · NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'
“A Python and R package for producing the figures and tables of this paper is available at https://github.com/saezlab/omnipath_analysis .”
A machine-resolvable code repository URL is given for the study's own code. [majority verdict 'yes' (3/4 passes agreed)]
NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code' · FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear · FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)
“the European Union Innovative Medicines Initiative TransQST (agreement No. 116030)”
An award number is attached to a named funder.
DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award · Crossref Funder Registry — canonical funder identifiers for funding metadata · RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco
Advisory · not in the published score
“To build OmniPath , we developed a free software, the pypath Python module ( https://github.com/saezlab/pypath , version 0.11.39).”
The paper names the specific software (pypath) and its version used to produce the data.
RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa · FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati · W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance
The paper does not name a documentation object (README, codebook, schema) that travels with the data; variable definitions are provided only in the article text and tables. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]
RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data' · NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.891
From this paper's citation signal
Citation Network Contribution
3.5
From 100 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
European Union Innovative Medicines Initiative TransQST
Grant: 116030
Translational quantitative systems toxicology to improve the understanding of the safety of medicines - Sofia: 116030
Federal Ministry of Education
Grant: 031L0181B
Deutsche Forschungsgemeinschaft
Grant: SA 3554/1‐2
UKRI|Biotechnology and Biological Sciences Research Council
Grant: BB/J004529/1
UKRI|Biotechnology and Biological Sciences Research Council
Grant: BB/P016774/1
UKRI|Biotechnology and Biological Sciences Research Council
Grant: BB/CSP17270/1
UK Research and Innovation|Biotechnology and Biological Sciences Research Council, ISP grant for Gut Microbes and Health
Grant: BB/R012490/1
UK Research and Innovation|Biotechnology and Biological Sciences Research Council, Norwich Research Park Biosciences Doctoral Training Partnership grant
Grant: BB/M011216/1
The Norwich Research Park Biosciences Doctoral Training Partnership
Biotechnology and Biological Sciences Research Council
Grant: BBS/E/F/000PR10355
Changes in gut microbe-host interactions and their impact beyond the gut
Biotechnology and Biological Sciences Research Council
Grant: BBS/E/T/000PR12374
Biotechnology and Biological Sciences Research Council
Grant: BBS/E/T/000PR9817
Biotechnology and Biological Sciences Research Council
Grant: 1940961
Biotechnology and Biological Sciences Research Council
Grant: BBS/E/T/000PR9818
Biotechnology and Biological Sciences Research Council
Grant: BBS/E/T/000PR9819
Deutsche Forschungsgemeinschaft (DFG)
Grant: SA 3554/1-2
Biotechnology and Biological Sciences Research Council
Grant: 1799901
UK Research and Innovation
Grant: BBS/E/F/000PR10353
Determinants of microbe-host responses in the gut across life
Deutsche Forschungsgemeinschaft
Grant: unidentified
unidentified
JRC COMBINE, partially funded by Bayer AG
JRC COMBINE, partially funded by Bayer AG
FWCI
18.28
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals