Skip to content

Commit

Permalink
Fixed typo for CIViC database
Browse files Browse the repository at this point in the history
  • Loading branch information
Genarito authored Mar 3, 2024
1 parent e73e701 commit bd4c865
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,16 +33,16 @@ BioAPI obtains information from different bioinformatics databases. These databa
HGNC is the resource for approved human gene nomenclature. Downloaded from its official website in September 2022.
2. Gene information:

- [ENSEMBL](http://www.ensembl.org/biomart/martview): BioMart data mining tool was used to obtain a gene-related dataset from Ensembl. Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotates genes, computes multiple alignments, predicts regulatory function and collects disease data. Downloaded using *BioMart data mining tool* in September 2022.
- [ENSEMBL](http://www.ensembl.org/biomart/martview): BioMart data mining tool was used to obtain a gene-related dataset from Ensembl. Ensembl is a genome browser for vertebrate genomes that supports comparative genomics, evolution, sequence variation and transcriptional regulation research. Ensembl annotates genes, computes multiple alignments, predicts regulatory function, and collects disease data. Downloaded using *BioMart data mining tool* in September 2022.
- [RefSeq](https://www.ncbi.nlm.nih.gov/refseq/): the summary of each human gene was obtained from the RefSeq database. RefSeq (Reference Sequence) is the public database of annotated and curated nucleic acid (DNA and RNA) and protein sequences from the National Center for Biotechnology Information (NCBI). To obtain the summaries, the R package called [GeneSummary](https://bioconductor.org/packages/release/data/annotation/html/GeneSummary.html) was used, which obtains the abstracts from version 214 of RefSeq.
- [CiVIC](https://civicdb.org/welcome): a description of the genes oriented to clinical interpretation in cancer was obtained from the CiVIC database, an open-source platform supporting crowd sourced and expert-moderated cancer variant curation. The database was downloaded from its official website in April 2023.
- [CIViC](https://civicdb.org/welcome): A description of the genes oriented to clinical interpretation in cancer was obtained from the CIViC database, an open-source platform supporting crowd-sourced and expert-moderated cancer variant curation. The database was downloaded from its official website in April 2023.

3. Metabolic pathways: [ConsensusPathDB](http://cpdb.molgen.mpg.de/).
ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from currently 31 public resources for interactions (listed below) and interactions that we have curated from the literature. The interaction data are integrated in a complementary manner (avoiding redundancies), resulting in a seamless interaction network containing different types of interactions. Downloaded from its official website in September 2022.
ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory, and drug-target interactions, as well as biochemical pathways. Data originate from currently 31 public resources for interactions (listed below) and interactions that we have curated from the literature. The interaction data are integrated in a complementary manner (avoiding redundancies), resulting in a seamless interaction network containing different types of interactions. Downloaded from its official website in September 2022.
4. Gene expression: [Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/).
The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 54 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. GTEx is being used in its version [GTEx Analysis V8 (dbGaP Accession phs000424.v8.p2)](https://gtexportal.org/home/datasets#datasetDiv1) and was downloaded from its official website in September 2022.
5. Therapies and actionable genes in cancer: [OncoKB](https://www.oncokb.org/).
OncoKB™ is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer. Alteration- and tumor type-specific therapeutic implications are classified using the OncoKB™ [Levels of Evidence system](https://www.oncokb.org/levels), which assigns clinical actionability to individual mutational events. Downloaded from its official website in November 2023.
OncoKB™ is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about cancer-related genomic alterations. Alterations and tumor-type-specific therapeutic implications are classified using the OncoKB™ [Levels of Evidence system](https://www.oncokb.org/levels), which assigns clinical actionability to individual mutational events. Downloaded from its official website in November 2023.
6. Gene Ontology [Gene Ontology (GO)](http://geneontology.org/).
It is a project to develop an up-to-date, comprehensive, computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems. It provides structured and standardized annotations of gene products, in a hierarchical system of terms and relationships that describes the molecular functions, biological processes, and cellular components associated with genes and gene products. Downloaded from its official website in June 2023
7. Cancer-related drugs [Pharmacogenomics Knowledge Base (PharmGKB)](https://www.pharmgkb.org/).
Expand Down Expand Up @@ -148,7 +148,7 @@ From a list of valid genes, it obtains different information for the human refer
- `strand`: DNA strand containing the coding sequence for the gene. Possible values are 1 for the positive strand or -1 for the negative strand.
- `gene_biotype`: A gene or transcript classification (examples: protein_coding or miRNA). The different possibilities for this field can be found in the [Biotype section of the Ensembl documentation](https://vega.archive.ensembl.org/info/about/gene_and_transcript_types.html).
- `refseq_summary`: complete description of the gene according to the RefSeq database (RefSeq : NCBI Reference Sequences).
- `civic_description`: Description of the clinical relevance of the gene according to the CiVIC (Clinical Interpretation of Variants in Cancer) database.
- `civic_description`: Description of the clinical relevance of the gene according to the CIViC (Clinical Interpretation of Variants in Cancer) database.
- `hgnc_id`: Gene identifier in the HGNC database.
- `uniprot_ids`: Gene identifier in the Uniprot database.
- `omim_id`: Gene identifier in the OMIM database.
Expand Down

0 comments on commit bd4c865

Please sign in to comment.