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Cited by 198Cancer Genomics and DiagnosticsCancer Cells and MetastasisResearch Data Management Practices

Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models

Open access
van der Meer, Dieudonne, Barthorpe, Syd, Yang, Wanjuan, Lightfoot, Howard, Hall, Caitlin, Gilbert, James, Francies, Hayley E, Garnett, Mathew J·2019·Nucleic Acids Research
DOI 10.1093/nar/gky872PMC PMC6324059
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Abstract

In vitro cancer cell cultures are facile experimental models used widely for research and drug development. Many cancer cell lines are available and efforts are ongoing to derive new models representing the histopathological and molecular diversity of tumours. Cell models have been generated by multiple laboratories over decades and consequently their annotation is incomplete and inconsistent. Furthermore, the relationships between many patient-matched and derivative cell lines have been lost, and accessing information and datasets is time-consuming and difficult. Here, we describe the Cell Model Passports database; cellmodelpassports.sanger.ac.uk, which provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. The Passports database currently contains curated details and standardized annotation for >1200 cell models, including cancer organoid cultures. The Passports will be updated with newly derived cell models and datasets as they are generated. Users can navigate the database via tissue, cancer-type, genetic feature and data availability to select a model most suitable for specific applications. A flexible REST-API provides programmatic data access and exploration. The Cell Model Passports are a valuable tool enabling access to high-dimensional genomic and phenotypic cancer cell model datasets empowering diverse research applications.

AI snapshot

Written from the paper’s full text.

TL;DR

Cell Model Passports is a database and web/API resource that curates >1200 cancer cell models, including organoids, with patient/sample/model relationships and links to genomic and drug sensitivity datasets. It aims to improve model selection, data integration, and reproducibility by standardizing annotation and identifiers.

Key findings

  • The Passports database contains curated details and standardized annotation for >1200 cell models, including cancer organoid cultures; over 30 attributes may be annotated per model, with lineage captured via 29 tissue categories, 44 cancer types, and 194 cancer type detail categories.
  • It provides >3500 genetic datasets and >1000 drug sensitivity datasets; 85% of cell models have associated somatic nucleotide variant, gene expression, copy number variation, or methylation datasets, and mutation status is provided for 455 cancer driver genes with drug profiling of ∼250 compounds from GDSC.
  • The resource captures patient–sample–model hierarchies and parent–child model relationships, using unique identifiers such as RRID, COSMIC, and CCLE, and STR/fingerprinting to confirm model–patient associations and reduce mis-identification.
  • Access is available through a web interface and a REST API following JSONAPI v1.0, with processed gene-level datasets and links to raw data.

Methods

  • Database construction used PostgreSQL v9.6 hosted at the Wellcome Sanger Institute; the REST API was developed in Python 3.6 with Flask v0.12 and SQLAlchemy v1.2, and the web interface used React v16.4 with Bootstrap v4.0.
  • Curation compiled information from commercial cell banks (ATCC, DSMZ, JCRB, ECACC), academic collaborators, Cellosaurus, CCLE, and publications; a constrained vocabulary was developed, and the patient/sample/model hierarchy was established using annotation plus resources cataloging mis-identified and synonymous models, with STR/fingerprinting to confirm associations.
  • The foundational model set includes >1200 established cancer cell lines and newly derived organoid models, including those used in the Sanger GDSC project and models from the Human Cancer Models Initiative; genomic features include microsatellite stability status, ploidy, mutational burden, and mutation status of 455 cancer driver genes.

Limitations

  • The paper states that currently all datasets have been generated by the Sanger Institute, and that the Passports currently focus on high quality and consistent datasets generated by the Wellcome Sanger Institute; future expansion to external resources is planned.
  • The paper states that the Passports will incorporate newly generated datasets from initiatives such as the Dependency Map at Sanger, indicating that some relevant datasets are not yet included.
  • Evident from the text: no formal user evaluation, benchmarking, or performance assessment of the web interface or API is reported; the paper is primarily descriptive of the resource.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/nar/gky872

Cites

42 of 42 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 32 cited sources checked · 0 supported · 0 flagged

  • Findingnone given

    Users can navigate the Passports database via tissue, cancer-type, genetic feature and data availability to select a model suitable for specific applications.

    “Users can navigate the database via tissue, cancer-type, genetic feature and data availability to select a model most suitable for specific applications.”
    Quote in the paperSubstantial claim
  • Findingnone given

    The Cell Model Passports is a central portal providing manual or programmatic access to a cancer cell model database containing curated patient, sample and model relationship information as well as genomic and functional datasets.

    “The Cell Model Passports is a central portal providing manual or programmatic access to a cancer cell model database containing curated patient, sample and model relationship information as well as genomic and functional datasets.”
    Quote in the paperSubstantial claim
  • Findingown data

    The Passports database currently contains curated details and standardized annotation for more than 1200 cell models, including cancer organoid cultures.

    “The Passports database currently contains curated details and standardized annotation for >1200 cell models, including cancer organoid cultures.”
    • Also stated in: § MODEL ANNOTATIONS · plain
      “More than 1200 established cancer cell lines and newly derived organoid models comprise the foundational model set of the Passports, including all those utilized in the Sanger’s GDSC project (5, 18) as well as cell models generated as part of the Human Cancer Models Initiative.”
    Quote in the paperSubstantial claim
  • Findingcitation

    The Passport model name is accompanied by synonyms and unique identifiers utilized by established resources such as RRID, COSMIC and CCLE to aid data integration and alignment.

    “The Passport model name is accompanied by synonyms and most importantly unique identifiers utilized by established resources such as Research Resource Identifiers (RRID) (19), the Catalogue of Somatic Mutations in Cancer (COSMIC) (20) and CCLE (6) to aid data integration and alignment.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [19] Bairoch, 2018, The Cellosaurus, a Cell-Line Knowledge Resource, J. Biomol. Tech. source

      Not checked in the free run.

    • cites [20] Forbes, 2017, COSMIC: somatic cancer genetics at high-resolution, Nucleic Acids Res. source

      Not checked in the free run.

    • cites [6] Barretina, 2012, The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature source

      Not checked in the free run.

  • Findingnone given

    The Passports currently focus on high quality and consistent datasets generated by the Wellcome Sanger Institute.

    “The Passports currently focus on high quality and consistent datasets generated by the Wellcome Sanger Institute, but in the future will expand to include cell models and datasets generated by external resources while maintaining an emphasis on quality and curation.”
    Quote in the paperNot a substantial claim
  • May combine two claims. 20
  • Classified as probably not a substantial claim. 15

  • May combine two claims.

    Findingcitation

    More than 1200 established cancer cell lines and newly derived organoid models comprise the foundational model set of the Passports, including all those utilized in the Sanger's GDSC project and cell models generated as part of the Human Cancer Models Initiative.

    “More than 1200 established cancer cell lines and newly derived organoid models comprise the foundational model set of the Passports, including all those utilized in the Sanger’s GDSC project (5, 18) as well as cell models generated as part of the Human Cancer Models Initiative.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [5] Garnett, 2012, Systematic identification of genomic markers of drug sensitivity in cancer cells, Nature source

      Not checked in the free run.

    • cites [18] Iorio, 2016, A landscape of pharmacogenomic interactions in cancer, Cell source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    A flexible REST-API provides programmatic data access and exploration.

    “A flexible REST-API provides programmatic data access and exploration.”
    • Also stated in: § API · plain
      “Programmatic access to the Cell Model Passports database is available through a flexible API.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Cell Model Passports database provides details of cell model relationships, patient and clinical information, and access to associated genetic and functional datasets.

    “Here, we describe the Cell Model Passports database; cellmodelpassports.sanger.ac.uk, which provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    All relationships between resources are fully annotated within the API, including API URLs to related resources.

    “To facilitate access to available resources, all relationships between resources are fully annotated within the API, including API URLs to related resources.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Over 3500 genetic datasets and more than 1000 drug sensitivity datasets are available in the Passports.

    “Over 3500 genetic datasets and more than 1000 drug sensitivity datasets are available.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    Any dataset values that were mapped to genes without an official gene symbol have been discarded from processing, but continue to be available in raw data downloads.

    “Any dataset values that were mapped to genes without an official gene symbol have been discarded from processing, but continue to be available in raw data downloads.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Findingreasoning

    The website enables users to search and/or filter for cell models via a variety of features as well as providing access to datasets.

    “The website enables users to search and/or filter for cell models via a variety of features as well as providing access to datasets.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    Cancer driver mutation status for a model is provided as a word cloud, where text size represents the prevalence of mutations in a gene for all cell models of the same tissue type, and the colour differentiates between tumour suppressors and oncogenes.

    “Cancer driver mutation status for a model is provided as a word cloud, where text size represents the prevalence of mutations in a gene for all cell models of the same tissue type, and the colour differentiates between tumour suppressors and oncogenes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    The search and filter functions allow users to conduct direct queries for an individual model or cancer and combine filters to identify a cohort of cell models with a particular set of characteristics.

    “The search and filter functions allow users to not only conduct direct queries for an individual model or cancer, but also combine filters to identify a cohort of cell models with a particular set of characteristics.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Models in the Passports have been derived from primary, metastatic, pre-cancerous and normal samples as indicated by 'Tissue Status', and the anatomical site from which the sample was obtained 'Sample Site' is also provided.

    “Models in the Passports have been derived from primary, metastatic, pre-cancerous and normal samples as indicated by ‘Tissue Status’, the anatomical site from which the sample was obtained ‘Sample Site’ is also provided.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    The Cell Model Passport is a centralized cell model hub, providing a platform for researchers to investigate key patient and sample information, manually and programmatically access multiple genetic and functional datasets, and facilitate integration of data from different sources through mapping of unique identifiers.

    “The Cell Model Passport is a centralized cell model hub, providing a platform for researchers to investigate key patient and sample information, manually and programmatically access multiple genetic and functional datasets, and facilitate integration of data from different sources through mapping of unique identifiers.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    Multiple information panels are displayed on the Model Page; 'Model Information' is provided for all models while additional panels are dependent upon availability of relevant information.

    “Multiple information panels are displayed on the Model Page (Figure 3). ‘Model Information’ is provided for all models while additional panels are dependent upon availability of relevant information.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    Processed datasets provide gene-level information, rather than segment or transcript, allowing direct integration and cross-comparisons with other datasets within the Passports.

    “The processed datasets provide gene-level information, rather than segment or transcript, allowing direct integration and cross-comparisons with other datasets within the Passports.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Findingnone given

    The processed files and a description of cancer driver gene status for each model facilitates access for non-informaticians.

    “The processed files and a description of cancer driver gene status for each model facilitates access for non-informaticians.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    Data files are hosted on a robust S3 object store platform or in third party repositories; the Cell Model Passport database contains links to these files together with associated metadata.

    “Data files are hosted on a robust S3 object store platform or in third party repositories; the Cell Model Passport database contains links to these files together with associated metadata.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Endpoints are available for lists of patients, samples, models, identifiers, files, all processed datasets and cancer driver mutations.

    “Endpoints are available for lists of patients, samples, models, identifiers, files, all processed datasets and cancer driver mutations.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Drug sensitivity data obtained from the GDSC project are reported showing the compounds to which a model is most sensitive.

    “Drug sensitivity data obtained from the GDSC project are also reported showing the compounds to which a model is most sensitive.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    There are two categories of files, each with their own database table: generic files and model files.

    “There are two categories of files, each with their own database table: generic files and model files.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The lack of a consistent controlled vocabulary to describe cell line metadata and the large number of synonymous identifiers makes data integration and cross-referencing of datasets burdensome.

    “The lack of a consistent controlled vocabulary to describe cell line metadata and the large number of synonymous identifiers makes data integration and cross-referencing of datasets burdensome (14, 15).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [14] Kurtz, 2018, A standard nomenclature for referencing and authentication of pluripotent stem cells, Stem Cell Rep. source

      Not checked in the free run.

    • cites [15] Yu, 2015, A resource for cell line authentication, annotation and quality control, Nature source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Key patient and clinical information, including relationships between cell lines originally derived from the same patient or sample, has been lost.

    “In addition, key patient and clinical information has been lost including relationships between cell lines originally derived from the same patient or sample (13).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [13] Vermeulen, 1998, Did the four human cancer cell lines DLD-1, HCT-15, HCT-8, and HRT-18 originate from one and the same patient, Cancer Genet. Cytogenet. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Many cancer cell models have been cross-contaminated or are associated with numerous synonymous identifiers.

    “Many models have inadvertently been cross-contaminated (9–11) or are associated with numerous synonymous identifiers (11, 12).”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [9] Gartler, 1968, Apparent Hela cell contamination of human heteroploid cell lines, Nature source

      Not checked in the free run.

    • cites [10] Nelson-Rees, 1974, Banded marker chromosomes as indicators of intraspecies cellular contamination, Science source

      Not checked in the free run.

    • cites [11] Lorsch, 2014, Cell Biology. Fixing problems with cell lines, Science source

      Not checked in the free run.

    • cites [12] Luong, 2011, A call for standardized naming and reporting of human ESC and iPSC lines, Cell Stem Cell source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    A clear understanding of the characteristics and source of the model used to generate a given dataset is important for reproducibility of results.

    “Therefore, a clear understanding of the characteristics and source of the model used to generate a given dataset is important for reproducibility of results.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductreasoning

    By default, models sharing common ancestry are assigned to separate samples of a single patient, unless evidence is available indicating otherwise; this conservative approach ensures data can be accurately attributed to the specific cell model, thereby improving reproducibility between users of the same or related models.

    “By default, models sharing common ancestry are assigned to separate samples of a single patient, unless evidence is available indicating otherwise. This relatively conservative approach ensures data can be accurately attributed to the specific cell model, thereby improving reproducibility between users of the same or related models.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Cellosaurus and cBioPortal do not provide cell model functional information, while PharmacoDB does not contain genomic annotation of the cell models and has limited sample/model information.

    “First, Cellosaurus and cBioPortal do not provide cell model functional information, while PharmacoDB does not contain genomic annotation of the cell models and has limited sample/model information.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [19] Bairoch, 2018, The Cellosaurus, a Cell-Line Knowledge Resource, J. Biomol. Tech. source

      Not checked in the free run.

    • cites [35] Smirnov, 2018, PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies, Nucleic Acids Res. source

      Not checked in the free run.

    • cites [36] Cerami, 2012, The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data, Cancer Discov. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Recent technological advancements (e.g. organoid models and conditionally reprogrammed cell lines) have led to a new generation of cancer cell models being derived to allow full representation of the histopathological and molecular diversity of tumours.

    “Furthermore, with recent technological advancements (e.g. organoid models and conditionally reprogrammed cell lines), a new generation of cancer cell models is being derived to allow full representation of the histopathological and molecular diversity of tumours (37–42).”
    Quote in the paperNot a substantial claim0 of 6 sources checked
    • cites [37] van de Wetering, 2015, Prospective derivation of a living organoid biobank of colorectal cancer patients, Cell source

      Not checked in the free run.

    • cites [38] Broutier, 2017, Human primary liver cancer-derived organoid cultures for disease modeling and drug screening, Nat. Med. source

      Not checked in the free run.

    • cites [39] Sachs, 2018, A living biobank of breast cancer organoids captures disease heterogeneity, Cell source

      Not checked in the free run.

    • cites [40] Tiriac, 2018, Organoid profiling identifies common responders to chemotherapy in pancreatic cancer, Cancer Discov. source

      Not checked in the free run.

    • cites [41] Boj, 2015, Organoid models of human and mouse ductal pancreatic cancer, Cell source

      Not checked in the free run.

    • cites [42] Nanki, 2018, Divergent routes toward Wnt and R-spondin niche independency during human gastric carcinogenesis, Cell source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductreasoning

    Currently, all datasets in the Passports have been generated by the Sanger Institute, and consequently there is a direct relationship between the cell model described and the datasets provided, mitigating the risk of mis-identification and genetic drift.

    “Currently, all datasets have been generated by the Sanger Institute and consequently there is a direct relationship between the cell model described and the datasets provided, mitigating the risk of mis-identification and genetic drift.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The Cell Model Passports provide a resource to reduce the mis-identification of cell models, facilitate data integration and subsequently improve experimental reproducibility in cancer research and related fields.

    “In summary, the Cell Model Passports provide a resource to reduce the mis-identification of cell models, facilitate data integration and subsequently improve experimental reproducibility in cancer research and related fields.”
    Quote in the paperSubstantial claim
27 of 27

  • The paper relies on this without support.

    Datasets associated with cell models are often inaccessible to non-computational, wet-lab scientists.

    “Furthermore, these datasets are often inaccessible to non-computational, wet-lab scientists.”

  • The paper relies on this without support.

    It is often difficult to determine what information is available for a particular cell line and how to access these data.

    “Although many cell lines have been genetically and functionally characterized, it is often difficult to determine what information is available for a particular cell line and how to access these data.”
2 of 2

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Fitness Scores calculated from large-scale genome-wide CRISPR/Cas9 screens across 31 independent CRC cell lines represent a quantitative measure of the reduction of cell viability elicited by gene inactivation via CRISPR/Cas9.

    “''Fitness Scores'' that were calculated from large-scale genome-wide CRISPR/Cas9 screens across 31 independent CRC cell lines and represent a quantitative measure of the reduction of cell viability elicited by a gene inactivation via CRISPR/Cas9 (https://score.depmap.sanger.ac.uk) (Behan et al., 2019;van der Meer et al., 2019).”

    From Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer (2021) · cites this paper as van der Meer et al., 2019

Cites

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Related

Authors
van der Meer, D., Barthorpe, S., Yang, W., Lightfoot, H., Hall, C., Gilbert, J., Francies, H. E., & Garnett, M. J.
Affiliations
  • Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
  • Wellcome Sanger Institute (GB)
Corresponding author
  • Francies, Hayley E
  • Garnett, Mathew J
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2018-09-27
Volume
47
Issue
D1
Pages
D923-D929
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gky872
PMC
PMC6324059
OpenAlex
W2893209354
Semantic Scholar
a3d79f0a93ca5e44a28c400635b41f824442ac63
Cited by
195
References
42
Citations by year
2026: 21 · 2025: 32 · 2024: 27 · 2023: 35 · 2022: 22 · 2021: 31 · 2020: 17 · 2019: 8 · 2018: 1
FWCI
4.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Cancer Research UK (C44943/A22536)
  • Stand Up To Cancer (SU2C-AACRDT1213)
  • Wellcome Trust (102696)
  • Wellcome Sanger Institute (206194)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
  • Health Sciences › Medicine › Oncology › Cancer Cells and Metastasis
  • Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
Keywords
cancer cell lines, preclinical cancer models, tumor organoids, REST API, database curation, drug development models
MeSH terms
Drug Development, Antineoplastic Agents, Humans, Models, Biological, Organoids, Databases, Factual, Genomics, Cell Line, Tumor, Datasets as Topic

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