Bgee Resource Ingest Guide¶
Source Information¶
InfoRes ID: infores:bgee
Description: Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species. It provides an intuitive answer to the question "where is a gene expressed?" and supports research in cancer and agriculture, as well as evolutionary biology. Bgee is built exclusively from curated "normal" (healthy wild-type) expression data - RNA-Seq, single-cell RNA-Seq, Affymetrix microarrays, in situ hybridization, and ESTs - which are uniformly reprocessed and integrated to produce present/absent expression calls for genes in anatomical entities (and developmental stages) across species, each with an associated confidence level and expression rank/score.
Citations: - Frederic B Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid H Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi, The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D831-D847, https://doi.org/10.1093/nar/gkaa793
Data Access Locations: - Bgee expression call downloads - https://www.bgee.org/ftp/current/download/calls/expr_calls/ (per-species gene expression call TSV files, one file per species) - Bgee gene expression calls download page - https://www.bgee.org/download/gene-expression-calls (human-facing download portal with per-species links and documentation) - Bgee release manifest - https://www.bgee.org/ftp/release_v2.tsv (tab-delimited manifest whose 'release' field the ingest reads to determine the current source version)
Data Provision Mechanisms: file_download
Data Formats: tsv
Data Versioning and Releases: Bgee issues numbered releases (e.g. v15.0, ingested here) on an irregular, as-needed cadence rather than on a fixed schedule. The ingest downloads from the "current" release path and reads the release version from the manifest file at https://www.bgee.org/ftp/release_v2.tsv.
Additional Notes: ['bgee.org returns HTTP 403 for the default Python urllib User-Agent, so the ingest sends a browser-like User-Agent when fetching the release manifest to determine the current version.']
Ingest Information¶
Ingest Categories: primary_knowledge_provider
Utility: The information provided by Bgee gives us insight into where genes are expressed - within specific cell types and anatomical locations - across a multitude of organisms. These gene-to-tissue/cell expression assertions support Translator query and reasoning use cases that need to know the anatomical and cellular context of gene activity.
Scope: Curated "present" gene expression calls linking genes to UBERON anatomical entities and CL cell types, restricted to high-confidence, strongly-signaled calls. Currently limited to human, mouse, and rat, and to the presence of expression only. Bgee provides various metrics (expression rank, expression score, FDR) that are used here to filter to the most reliable calls.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| Homo_sapiens_expr_simple.tsv.gz | https://www.bgee.org/ftp/current/download/calls/expr_calls/Homo_sapiens_expr_simple.tsv.gz | Homo sapiens (human) gene expression calls. |
| Rattus_norvegicus_expr_simple.tsv.gz | https://www.bgee.org/ftp/current/download/calls/expr_calls/Rattus_norvegicus_expr_simple.tsv.gz | Rattus norvegicus (brown rat) gene expression calls. |
| Mus_musculus_expr_simple.tsv.gz | https://www.bgee.org/ftp/current/download/calls/expr_calls/Mus_musculus_expr_simple.tsv.gz | Mus musculus (house mouse) gene expression calls. |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| Homo_sapiens_expr_simple.tsv.gz | Rows where Expression is "present" and the call passes the confidence filters (Expression rank < 10000, Expression score > 70, FDR < 0.05). Each included row asserts that a gene is expressed in a given anatomical entity (UBERON) or cell type (CL) in human. | Gene ID, Anatomical entity ID, Expression, Call quality, FDR, Expression score, Expression rank |
| Rattus_norvegicus_expr_simple.tsv.gz | Rows where Expression is "present" and the call passes the confidence filters (Expression rank < 10000, Expression score > 70, FDR < 0.05). Each included row asserts that a gene is expressed in a given anatomical entity (UBERON) or cell type (CL) in rat. | Gene ID, Anatomical entity ID, Expression, Call quality, FDR, Expression score, Expression rank |
| Mus_musculus_expr_simple.tsv.gz | Rows where Expression is "present" and the call passes the confidence filters (Expression rank < 10000, Expression score > 70, FDR < 0.05). Each included row asserts that a gene is expressed in a given anatomical entity (UBERON) or cell type (CL) in mouse. | Gene ID, Anatomical entity ID, Expression, Call quality, FDR, Expression score, Expression rank |
Filtered Content¶
| File Name | Filtered Records | Rationale |
|---|---|---|
| Homo_sapiens_expr_simple.tsv.gz | 'Expression rank' >= 10,000 OR 'Expression score' <= 70 OR 'FDR' >= 0.05 OR 'Expression' != "present" (i.e. "absent" calls) | We are specifically targeting gene expression calls which are strongly signaled and highly probable. Any calls which have a low score or are potentially spurious, and all "absent" (not-expressed) calls, are filtered. |
| Rattus_norvegicus_expr_simple.tsv.gz | 'Expression rank' >= 10,000 OR 'Expression score' <= 70 OR 'FDR' >= 0.05 OR 'Expression' != "present" (i.e. "absent" calls) | We are specifically targeting gene expression calls which are strongly signaled and highly probable. Any calls which have a low score or are potentially spurious, and all "absent" (not-expressed) calls, are filtered. |
| Mus_musculus_expr_simple.tsv.gz | 'Expression rank' >= 10,000 OR 'Expression score' <= 70 OR 'FDR' >= 0.05 OR 'Expression' != "present" (i.e. "absent" calls) | We are specifically targeting gene expression calls which are strongly signaled and highly probable. Any calls which have a low score or are potentially spurious, and all "absent" (not-expressed) calls, are filtered. |
Future Content Considerations¶
edge_content: Filter some organisms which are already filtered by Monarch. In general, explore prior Monarch ingest of this source to see what we can learn/borrow. And reach out to F. Bastian to get a better understanding of the source and its utility for Translator use cases. - Relevant files: Caenorhabditis_elegans_expr_simple.tsv.gz, Danio_rerio_expr_simple.tsv.gz, Drosophila_melanogaster_expr_simple.tsv.gz, Mus_musculus_expr_simple.tsv.gz, Rattus_norvegicus_expr_simple.tsv.gz, Xenopus_laevis_expr_simple.tsv.gz
edge_content: Add in more model organisms. [Danio_rerio_expr_simple.tsv.gz Danio rerio (zebra fish), Xenopus_laevis_expr_simple.tsv.gz Xenopus laevis (African clawed frog), Drosophila_melanogaster_expr_simple.tsv.gz Drosophila melanogaster (fruit fly), Caenorhabditis_elegans_expr_simple.tsv.gz Caenorhabditis elegans (roundworm), Canis_lupus_familiaris_expr_simple.tsv.gz Canis lupus familiaris (dog), Bos_taurus_expr_simple.tsv.gz Bos taurus (cattle), Sus_scrofa_expr_simple.tsv.gz Sus scrofa (wild boar), Gallus_gallus_expr_simple.tsv.gz Gallus gallus (red junglefowl)]. - Relevant files: Danio_rerio_expr_simple.tsv.gz, Xenopus_laevis_expr_simple.tsv.gz, Drosophila_melanogaster_expr_simple.tsv.gz, Caenorhabditis_elegans_expr_simple.tsv.gz, Canis_lupus_familiaris_expr_simple.tsv.gz, Bos_taurus_expr_simple.tsv.gz, Sus_scrofa_expr_simple.tsv.gz, Gallus_gallus_expr_simple.tsv.gz
edge_content: Add qualifying developmental stage information. - Relevant files: all
edge_content: Add edges describing over/under expression of genes in specific tissues. And info indicating when a gene is ubiquitously expressed. - Relevant files: all
edge_property_content: Add in incorporation of Expression rank, Expression score, and FDR as edge properties. These values are currently used only for filtering and are not emitted on the output edges. - Relevant files: all
edge_content: Learn about meaning/utility of scores, and consider applying filters to focus on subset that is most meaningful/useful for Translator. - Relevant files: all
Target Information¶
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:Gene | biolink:AnatomicalEntity, biolink:Cell | knowledge_assertion | automated_agent | Bgee data provide Gene-Tissue/Cell expression assertions generated by uniformly reprocessing healthy RNA-Seq, single-cell RNA-Seq, microarray, EST, and in situ hybridization datasets, applying statistical thresholds to call expression presence/absence within experiments, and integrating evidence across studies and data types - followed by ontology-based propagation - to produce a single consensus expression call with an associated confidence level. This ingest keeps only high-confidence "present" calls and represents each as a Gene 'expressed_in' AnatomicalEntity (UBERON) or Cell (CL) edge. |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:Gene | ENSEMBL | |
| biolink:Cell | CL | |
| biolink:AnatomicalEntity | UBERON |
Future Modeling Considerations¶
edge_properties: Attach Bgee's Expression rank, Expression score, and FDR to each edge as edge properties, to convey the strength and confidence of each expression call. These values are currently used only for filtering.
qualifiers: Add developmental-stage context (and potentially anatomical/species context) as edge qualifiers once stage information is ingested, so that expression calls can be scoped to a life stage.
Provenance Information¶
Contributors: - Daniel Korn: code author - Kevin Schaper: code support - Evan Morris: code support - Sierra Moxon: code support - Matthew Brush: data modeling, domain expertise
Artifacts: - Ingest Survey: https://docs.google.com/spreadsheets/d/1bx4OSH1_HR69sKXIL1UBbelbUEx8X0b-gZTi8F81ypo/ - Ingest Ticket: https://github.com/NCATSTranslator/Data-Ingest-Coordination-Working-Group/issues/54