Biological Databases, Standards & Ontologies

Gain expertise in curated biological databases, FAIR data standards, and ontology-driven annotations through real-world practical sessions.

Biological Databases, Data Standards & Ontologies

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Session Index

Session 1 — Core DBs, FAIR & Metadata Session 2 — Standards & Ontologies Session 3 — Curation & Submissions Session 4 — Mini Capstone: KG Build

Session 1

Fee: Rs 4500

Core DBs, FAIR & Metadata

Landscape of primary & secondary biological databases

NCBI EMBL-EBI UniProt Ensembl

FAIR principles & minimal information checklists

MIxS MINSEQE FAIR

Accessioning, identifiers & cross-references

BioSample BioProject Accession

Programmatic access & rate-limits

EDirect Entrez API EBI APIs

Session 2

Fee: Rs 6000

Standards & Ontologies

Data models & schemas for sequence, variant & sample data

FASTQ/VCF/GFF3 JSON/JSON-LD RO-Crate

Ontology basics & evidence codes

OBO Foundry GO SO ECO

Semantic web tooling & validation

OWL RDF SHACL SPARQL

Practical term mapping & annotation pipelines

InterPro BioPortal OntoRunner

Session 3

Fee: Rs 8000

Curation & Submissions

Metadata templates & validator tooling

ENA Webin SRA GEO

Versioning, provenance & audit trails

Git RO-Crate PROV-O

Automation for bulk loads & updates

Python pandas curl

Session 4

Fee: Rs 10000

Mini Capstone: Knowledge Graph Build

Designing semantic model & entity alignment

Theory

Ingest from ENA/GEO with validated metadata

EDirect GEOquery Webin-CLI

Triple store load & competency queries

GraphDB Blazegraph SPARQL

Final report preparation and defense

Quarto JupyterLab pandas

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Biological Databases, FAIR Standards & Ontologies Training | Hands-on Module

Biological Databases, Standards & Ontologies