调研与学习技能

Retrieve evolutionary conservation scores and transcription factor binding sites from UCSC Genome Browser. Examine how genomic positions have changed across species and locate sites where gene-regulating proteins may bind, supporting analysis of variants and regulatory regions.

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• Checking conservation at single-nucleotide variants
• Finding conservation peaks across regulatory regions
• Looking up transcription factor binding sites in a region

Search open-access life-science literature in Europe PMC by keyword, author, or article identifier. Download available PDFs and full texts as plain text or XML, and retrieve reference lists and papers that cite a study.

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• Find open-access papers on a life-science topic
• Look up a paper by DOI or PMID
• Save full text as PDF, plain text, or XML

Retrieve protein and nucleotide sequences from NCBI using accession numbers, gene names, organisms, locus tags, PubMed articles, or patent numbers. Translate coding regions into protein sequences and search by organism and expected length when other identifiers are unavailable.

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• Retrieving sequences by accession number
• Finding proteins by gene name or locus tag and organism
• Collecting protein sequences linked to papers or patents

Find datasets of direct interactions between DNA and transcription factors, proteins that regulate gene activity, in UniBind. Filter by species, cell line, or factor name, inspect dataset details, and download binding sites as BED or FASTA files.

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• Find binding datasets for a transcription factor
• List datasets for a species or cell line
• Inspect dataset details and data sources

Search ChEMBL for compounds, drug targets, and measured biological activity. Retrieve drug mechanisms, compare activity values in a common unit, find similar chemical structures, and download structure files or images for further analysis.

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• Find compounds and their drug targets
• Compare IC50 values in a common unit
• Check drug mechanisms and indications

Retrieve preprint metadata from bioRxiv and medRxiv using a known DOI or a short date range and subject category. Filter results by keywords or author, optionally include abstracts, and save the matching records as JSON.

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• Retrieving paper metadata from a known DOI
• Reviewing preprints from a specific period and subject
• Filtering a short period by keywords or author

Search UniProt for proteins and retrieve their functions, amino acid sequences, organism information, and linked publications. Convert identifiers between databases, collect large sets of records, or retrieve earlier versions of protein entries.

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• Looking up protein functions and amino acid sequences
• Converting protein identifiers between databases
• Collecting protein annotations in bulk

Analyze Latin and Ancient Greek inscriptions to restore missing characters, estimate their place and date of origin, and find parallel texts. Review model predictions in tables and an HTML dashboard, with optional numerical text representations for further analysis.

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• Restoring missing characters in ancient inscriptions
• Estimating where and when an ancient text originated
• Finding parallel inscriptions for comparison

Search PubMed for biomedical papers and published clinical trials, retrieve abstracts and open-access full text, and connect papers with gene or compound records. Resolve incomplete citations and retrieve larger sets of references in batches.

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• Find biomedical papers and published clinical trials
• Retrieve abstracts and open-access full text
• Explore papers linked to specific genes or compounds

Align multiple protein sequences with EBI Clustal Omega and save the results locally. Compare sequence identity, examine conserved regions that remain unchanged across proteins, and map known functional residues to corresponding positions in the alignment.

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• Comparing multiple protein sequences
• Checking conservation of known functional residues
• Comparing a protein fragment with a full-length sequence

Retrieve gene RNA expression levels across 54 adult, non-diseased tissue sites from GTEx. Compare tissues, find where a gene is most active, and obtain eQTLs, genetic variants associated with differences in expression.

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• Compare a gene’s RNA expression across tissues
• Find tissues with the highest expression of a gene
• Retrieve eQTLs associated with a gene

Search PubChem by chemical name, identifier, or molecular structure to retrieve properties, hazards, and pharmacology information. Find similar molecules or compounds containing a chosen structural fragment, and retrieve structure images and biological assay data.

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• Checking a compound's properties and alternative names
• Finding molecules with similar structures
• Looking up chemical hazards and handling precautions

Find DNA binding profiles for transcription factors, proteins that regulate genes, in JASPAR. Resolve gene names to matrix IDs, retrieve binding patterns and metadata, and export profiles in formats used by sequence analysis tools.

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• Retrieve DNA binding patterns for a transcription factor
• Resolve gene names to JASPAR matrix IDs
• Convert frequency matrices to binding scores

Look up human proteins in the Human Protein Atlas to see their abundance by tissue and location within cells. Retrieve expression levels reported as categories, search for matching genes, and compare protein findings with RNA expression data.

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• Checking protein abundance across human tissues
• Finding where a protein is located within cells
• Comparing RNA and protein expression

Analyze a genetic variant with the AlphaGenome API to predict changes in gene activity, DNA accessibility, and RNA splicing, the joining of RNA segments. Produce comparison plots and a report highlighting effects across tissues.

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• Explore predicted effects of non-coding genetic variants
• Compare predicted gene activity changes across tissues
• Visualize changes in RNA splicing

Query QuickGO to connect genes with biological processes, molecular functions, and cellular locations. Find genes linked to a functional term, explore relationships between terms, and check the evidence supporting each annotation.

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• Look up a gene’s functions
• Find genes associated with a GO term
• Explore definitions and relationships of GO terms

Explore ENCODE data to find candidate DNA regions that regulate gene activity. Retrieve cell-specific annotations, nearby or linked genes, gene expression measurements, and experiment or file records, including ChIP-seq peaks, through the supplied scripts.

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• Finding candidate regulatory regions at genomic coordinates
• Checking genes near or linked to a regulatory region
• Comparing gene expression across biosamples

Search ClinicalTrials.gov for studies by condition, treatment, location, recruitment status, or trial phase. Retrieve individual trial details and participation criteria, count matching studies, and explore trials run by a particular company or institution.

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• Finding recruiting trials by condition and location
• Checking trial participation and exclusion criteria
• Counting studies by condition, phase, or time period

Look up short genetic variants in NCBI's dbSNP database. Connect rsIDs, identifiers for known variants, with genomic coordinates and HGVS variant descriptions, retrieve associated genes and allele frequencies, or search a chromosome region.

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• Find a known variant's rsID from genomic coordinates
• Check associated genes and allele frequencies for an rsID
• Convert an HGVS variant description to genomic coordinates

Query STRING to find protein interaction partners, examine supporting evidence and confidence scores, and identify biological pathways overrepresented in a protein list. It also supports homology searches and enrichment analysis using ranked experimental measurements.

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• Finding interaction partners for a protein
• Checking interaction evidence and confidence scores
• Identifying pathways overrepresented in a protein list

Explore disease-associated genes and known drugs using Open Targets Platform. Retrieve genetic evidence, predictions linking variants to genes, and information on whether a target can be addressed by drugs, including available safety data.

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• Find target genes associated with a disease
• Review druggability and safety information for a target
• Look up drugs and clinical candidates for a disease

Search openFDA for adverse event reports, recalls, labeling, approvals, and other regulatory records covering drugs, devices, foods, and more. Summarize field counts and download matching records as JSON files for further analysis.

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• Search adverse event reports for a drug
• Check recall records for devices or foods
• Look up drug labeling and NDC records

Look up genes in Ensembl, translate identifiers between biological databases, and retrieve DNA or protein sequences. The skill also provides transcript structures and VEP predictions, which describe possible molecular effects of genetic variants.

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• Resolving gene names or aliases to Ensembl IDs
• Mapping IDs to UniProt, HGNC, or RefSeq
• Retrieving DNA and protein sequences

Find research papers and preprints on arXiv, collect titles, authors, abstracts, and publication details, and save available PDFs, HTML full texts, or LaTeX source files. Search by topic, author, date, or a specific arXiv ID.

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• Find papers on a research topic
• Check abstracts and publication details
• Download a paper by arXiv ID