The document discusses the integration of big datasets related to biological data, detailing various datasets, their licenses, and the quantity of triples involved. It emphasizes the importance of data licensing and interoperability following Creative Commons standards for users and publishers. Additionally, it highlights challenges in quantitative data quality and the need for effective data governance within biological studies.

1. The Data Today
Alasdair Gray
Heriot-Watt University, Edinburgh, UK
A.J.G.Gray@hw.ac.uk
@gray_alasdair

2. @gray_alasdair Big Data Integration 2

3. Dataset Downloaded Version Licence Triples
Bio Assay Ontology CC-By 10,360
CALOHA 8 Apr 2015 2014-01-22 CC-By-ND 14,552
ChEBI 4 Mar 2015 125 CC-By-SA 1,012,056
ChEMBL 18 Feb 2015 20.0 CC-By-SA 445,732,880
ConceptWiki 12 Dec 2013 CC-By-SA 4,331,760
DisGeNET 31 Mar 2015 2.1.0 ODbL 15,011,136
Disease Ontology 2015-05-21 CC-By 188,062
DrugBank 19 Feb 2015 4.1 Non-commercial 4,028,767
ENZYME 2015_11 CC-By-ND 61,467
FDA Adverse Events 9 Jul 2012 CC0 13,557,070
Total: ~3 Billion triples

4. Dataset Downloaded Version Licence Triples
Gene Ontology 4 Mar 2015 CC-By 1,366,494
Gene Ontology Annotations 17 Feb 2015 CC-By 879,448,347
NCATS OPDDR Nov 2015 Oct 2015 2,643
neXTProt (NP) 1 Feb 2014 1.0 CC-By-ND 215,006,108
OPS Chemical Registry 4 Nov 2014 CC-By-SA 241,986,722
HMDB 3.6 HMDB
MeSH 2015 MeSH
PDB Ligands 2 PDB
OPS Metadata CC-By-SA 2,053
UniProt 2015_11 CC-By-ND 1,131,186,434
WikiPathways 20151118 CC-By 11,781,627
Total: ~3 Billion triples

5. John Wilbanks consulted for us
A framework built around STANDARD well-understood
Creative Commons licences – and how they interoperate
Deal with the problems by:
Interoperable licences
Appropriate terms
Declare expectations to users and
data publishers
One size won‘t fit all requirements
Data Licensing (Or Lack Of!)

6. Disease
Tissue
Target
Compound
Pathway

7. STANDARD_TYPE UNIT_COUNT
---------------- -------
AC50 7
Activity 421
EC50 39
IC50 46
ID50 42
Ki 23
Log IC50 4
Log Ki 7
Potency 11
log IC50 0
STANDARD_TYPE STANDARD_UNITS COUNT(*)
------------------ ------------------ --------
IC50 nM 829448
IC50 ug.mL-1 41000
IC50 38521
IC50 ug/ml 2038
IC50 ug ml-1 509
IC50 mg kg-1 295
IC50 molar ratio 178
IC50 ug 117
IC50 % 113
IC50 uM well-1 52
~ 100 units
>5000 types
Implemented using the Quantities, Units, Dimension, Types
Ontology (http://www.qudt.org/)
Quantitative Data Challenges

8. Quality Assurance

9. ops:OPS437281
✔
ops:OPS380297 ops:OPS380292
is_stereoisomer_of
[ci:CHEMINF_000461]
has_stereoundefined_parent
[ci:CHEMINF_000456] Other relationships
• has part
• is tautomer of
• uncharged counterpart
• isotope
…
Chemical Registration Service Data

10. Mappings: Raw
Mappings (Raw)
25,087,328

11. Mappings: Computed
Mappings (Comp)
200,000,000+

12. P12047
X31045
GB:29384
Andy Law's Third Law
“The number of unique identifiers assigned to an individual is
never less than the number of Institutions involved in the study”
http://bioinformatics.roslin.ac.uk/lawslaws/

13. DrugbankChemSpider PubChem
MesylateImatinib Mesylate
YLMAHDNUQAMNNX-UHFFFAOYSA-N
Are these records the same?
It depends upon your task!

14. skos:exactMatch
(InChI)
Strict Relaxed
Analysing Browsing
I need to perform an analysis, give me
details of the active compound in Gleevec.

15. skos:closeMatch
(Drug Name)
skos:closeMatch
(Drug Name)
skos:exactMatch
(InChI)
Strict Relaxed
Analysing Browsing
Which targets are known to interact
with Gleevec?

16. A lens defines a conceptual view over the data
Specifies operational equivalence conditions
Consists of:
Identifier (URI)
Title
(dct:title)
Description
(dct:description)
Documentation link
(dcat:landingPage)
Creator
(pav:createdBy)
Timestamp
(pav:createdOn)
Equivalence rules
(bdb:linksetJustification)
Scientific Lens
Lenses
34 in total
7 Public
25 Chemistry
2 Gene

21. Data Governance
Contribution must not be underestimated!!!

22. Alasdair J G Gray
A.J.G.Gray@hw.ac.uk
www.macs.hw.ac.uk/~ajg33/
@gray_alasdair
Open PHACTS
contact@openphacts.org
openphacts.org
@open_phacts