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Provenance in
a Collaborative Bio-database
RAASWiki
Donald Dunbar & Jon Manning
Queen’s Medical Research Institute
University of Edinburgh
Use Cases for Provenance
April 20th 2009
Provenance in
Bio-databases
including RAASWiki
Donald Dunbar & Jon Manning
Queen’s Medical Research Institute
University of Edinburgh
Use Cases for Provenance
April 20th 2009
Plan
bio-databases
RAASWiki
collaborative
knowledgebases
provenance
Biological databases
• Sequences
– Ensembl, Entrez
• Structure
– PDB
• Expression
– GEO, ArrayExpress
– Function
– Gene Ontology
– Interaction
– MINT, BIND, KEGG
– ‘Warehouses’
– GeneCards, IUPHAR
– Literature
– Pubmed
How do they handle provenance?
Ensembl produces genome databases for vertebrates and other eukaryotic
species, and makes this information freely available online.
‘Gene’ ID histories (with stable ID)
Evidence for gene predictions
Links to other databases (eg Uniprot)
How do they handle provenance?
The PDB archive contains information about experimentally-determined
structures of proteins, nucleic acids, and complex assemblies.
Primary citation
History: deposition and last update
Raw data and protocols
How do they handle provenance?
Gene Expression Omnibus: a gene expression/molecular abundance
repository supporting MIAME compliant data submissions, and a curated,
online resource for gene expression data browsing, query and retrieval.
Standards compliance (protocols, data…)
Links within database (microarrays, protocols)
Raw data and protocols
How do they handle provenance?
The Gene Ontology project provides a controlled vocabulary to describe
gene and gene product attributes in any organism.
Evidence for gene annotation (experimental, computational)
Links to original publications
No versioning, just updates
How do they handle provenance?
PubMed is a free search engine for accessing the MEDLINE database of
citations, abstracts and some full text articles on life sciences and
biomedical topics.
Original source material, authors, abstracts
Unique Pubmed ID (used by other databases)
Continual updates (new papers), occasional retractions
How do they handle provenance?
GeneCards® is a searchable, integrated database of human genes that
provides concise genomic, proteomic, transcriptomic, genetic and
functional information on all known and predicted human genes.
Lots of data from other databases
IDs/keys from sources
Lots of data integration based on IDs
How do they handle provenance?
The IUPHAR database (IUPHAR-DB) integrates peer-reviewed
pharmacological, chemical, genetic, functional and anatomical information
on GPCRs, ligand-gated ion channels and voltage-gated-like ion channel
subunits encoded by the human, rat and mouse genomes.
Curated by experts
Original sources plus curation provenance
Suggested citations
Newer developments
WikiGenes is the first wiki system to
combine the collaborative and largely
altruistic possibilities of wikis with
explicit authorship. In view of the
extraordinary success of Wikipedia
there remains no doubt about the
potential of collaborative publishing, yet
its adoption in science has been
limited. Here I discuss a dynamic
collaborative knowledge base for the
life sciences that provides authors
with due credit and that can evolve
via continual revision and traditional
peer review into a rigorous scientific
tool.
but….
RAASWiki
Important biology
- hypertension
RAASWiki is a knowledgebase of information
on the renin-angiotensin-aldosterone
system. While much of the seed data were
derived from pre-existing databases such as
KEGG and OMIM, supplementary data are
included not easily available through such
resources. This includes short textual reports
on the genes involved, and more
experimentally-oriented information such as
animal models.
Automatic seeding of database (BioKB)
Collaborative editing (Wiki based, useful functionality)
Genes, publications, animal models, datasets…
RAASWiki – provenance
Seeded data tagged with source database and date
Edits are tagged with editor and date
Comments are tagged: name and date
Wiki functionality allows versioning and roll back
Identifiers for source databases preserves provenance
‘Crowd wisdom’ will hopefully unsure good quality
RAASWiki – provenance issues
How much detail (each edit, granularity, versions)?
Who will use provenance data?
Different focus depending on data (who, when, confidence)
How much should we rely on sources for provenance?
Annotation & comments v changing data
Public v private data
Likely to become a big issue
What provenance to we need?
Example:
Gene expression in a transgenic animal
gene expression measurements
gene annotation
where, when
public databases
which identifiers
integration
when, what, how
output from machine
how
processing
what and how did we select genes
data mining
…
What provenance to we need?
Example:
Curated gene database
database links
curation
contributor, date
curator input
source, identifiers, dates
development
verify, add, delete, modify
archive
versions, dates
Curated database
schema & interface changes
Collaborative knowledgebases
databases
experiments
knowledge
papers
knowledgebase
Collaborative knowledgebase
provenance issues
Confidence in data
Tracking data to its (real) source
Published papers do not contain all information
When is something (knowledge) finished
Citing of knowlegebase records
Linking between knowledgebase records
Some sort of dynamic publication
Conclusions
•
•
•
•
•
In biology provenance is a mixed bag
We use mainly static databases
Usually source is clear but not much else
RAASWiki contains static and curated data
We have implemented a very rudimentary
provenance scheme
• Collaborative knowledgebases will need to
address provenance in new ways