Precise Structure-Based Criteria for Molecular Identity

1. Accurate biochemical knowledge starting with precise structure-based criteria for molecular identity Michel Dumontier, Ph.D. Assistant Professor of Bioinformatics Department of Biology, School of Computer Science Institute of Biochemistry, Ottawa Institute of Systems Biology Carleton University NCBO Seminar Series::Michel Dumontier

2. Problem Statement (I) • Although biochemical events can be described with reference to specific chemical substances, we may want to describe them at finer/grainier levels of (mereological) granularity. • residue : post translational modification • collection of residues : motif/domain/interaction site • atom : atomic interactions, catalytic mechanism • collection of atoms : binding/catalytic site, interaction • This requires identifiers for parts, regions (contiguous and non-contiguous), aggregates/complexes. • However, we do not (AFAIK) have a precise (reproducible) methodology to automatically generate these! NCBO Seminar Series::Michel Dumontier

3. Bio2RDF: 2.3B triples of SPARQL-accessible linked biological data! Chemical Parts!

4. Case Study: HIF1α Multiple hydroxylations Part of a domain • Context Dependent Behavior • Normoxic Conditions • Hypoxic Conditions The part is the agent in the process Selective interaction with parts Hypoxia-Inducible Factor 1, alpha chain (uniprot:Q16665) Master transcriptional regulator of the adaptive response to hypoxia • Under normoxic conditions, HIF1α is hydroxylated on Pro-402 and Pro-564 in the oxygen-dependent degradation domain (ODD) by EGLN1/PHD1 and EGLN2/PHD2. EGLN3/PHD3 has also been shown to hydroxylate Pro-564. The hydroxylated prolines promote interaction with VHL, initiating rapid ubiquitination and subsequent proteasomal degradation. NCBO Seminar Series::Michel Dumontier

5. Are these the same? • HIF1α – au naturel • HIF1α • hydroxylated @P402 • HIF1α • hydroxylated @P564 • HIF1α • hydroxylated @P402 & @P564 • HIF1α • hydroxylated @P402 & (@P564) • ubiquitinated @Lys-532 • HIF1α • L400A & L397A NCBO Seminar Series::Michel Dumontier

6. NO!!!! These are structurally different Each exhibits distinct functionality! Yet most databases (Uniprot/Genbank) don’t have separate identifiers for them Reactome has an internal identifier for referring to different forms, but links to Uniprot entries and doesn’t provide an explicit description of the structure that it corresponds to! NCBO Seminar Series::Michel Dumontier

7. So We have a clear need for being able to refer to distinct biochemical entities, based at least on their structure. We also need to refer to arbitrary structural parts. Should we generate all the combinations a priori???  NO!! Should we be able to automatically generate the identifier from the structural attributes? -> YES!!! Should we semantically annotate (manually or otherwise) those forms known to be involved in specific processes??? -> YES!!! What identifiers are unique for a given structure? NCBO Seminar Series::Michel Dumontier

8. InChI • IUPAC International Chemical Identifier (InChI) • A data string that provides • the structure of a chemical compound • the convention for drawing the structure • Different compounds must have different identifiers. Several attributes can be used to distinguish one compound from another. • chemical graph (connection table) • Formula • Atom type (only some atoms explicit) • Bond type • Stereochemistry • Mobile/fixed H-bonds (tautomers) • Isotopic composition • Atomic charge NCBO Seminar Series::Michel Dumontier

9. (S)-Glutamic Acid InChI= {version}1 /{formula}C5H9NO4 /c{connections}6-3(5(9)10)1-2-4(7)8 /h{H_atoms}3H,1-2,6H2,(H,7,8)(H,9,10) /p{protons}+1 /t{stereo:sp3}3- /m{stereo:sp3:inverted}0 /s{stereo:type (1=abs, 2=rel, 3=rac)}1 /i{isotopic:atoms}4+1 NCBO Seminar Series::Michel Dumontier

10. More non-core info captured in “AuxInfo” string... AuxInfo=1/1/N:5,6,2,7,1,4,8,9,10,11/E:(7,8)(9,10)/it:im/I:/E:m/rA:11nCCHN+CCC.i13OOOO/rB:s1;N2;P2;s2;s5;s6;s7;d7;d1;s1;/rC:6.1671,-19.3365,0;7.0125,-18.4864,0;6.4113,-17.4485,0;7.6089,-17.4485,0;7.8578,-19.3318,0;8.891,-18.7306,0;9.7363,-19.576,0;9.7316,-20.7735,0;10.8916,-19.266,0;5.0071,-19.0265,0;6.1624,-20.534,0; AuxInfo= {version}1 /{normalization_type}1 /N:{original_atom_numbers}5,6,2,7,1,4,8,9,10,11 /E:{atom_equivalence}(7,8)(9,10) /it:{abs_stereo_inverted:sp3}im /I:{isotopic:original_atom_numbers} /E:{isotopic:atom_equivalence}m /rA:{reversibility:atoms}11nCCHN+CCC.i13OOOO /rB:{reversibility:bonds}s1;N2;P2;s2;s5;s6;s7;d7;d1;s1; /rC:{reversibility:xyz}6.1671,-19.3365,0;7.0125,-18.4864,0;6.4113,-17.4485,0;7.6089,-17.4485,0;7.8578,-19.3318,0;8.891,-18.7306,0;9.7363,-19.576,0;9.7316,-20.7735,0;10.8916,-19.266,0;5.0071,-19.0265,0;6.1624,-20.534,0; NCBO Seminar Series::Michel Dumontier

11. So... InChi a really just a cryptic data identifier Clever software required to gradually build the chemical identifiers in a series of well-defined steps – normalization, canonicalization then serialization Humans can’t (easily) generate them nor can they easily understand them. But that’s OK. It’s not (user) extensible. But that’s OK. NCBO Seminar Series::Michel Dumontier

12. InCHI for Proteins??? • Possible... but a 1000 residue protein would contain ~15,000 atoms on average.... • OpenBabel seemed to struggle with anything over 100 residues • Maybe needs some performance tweaking? • Size of the string will be enormous • We can use InChiKeys (SHA1 hash), but then we need to provide a you-submit-InChI, we-store-both and they-look-it-up service. • Modularize InChI construction for (linear) polymers? • Make InChi strings for each residue, and concatenate – rename the atoms according to the residue position • We still need to translate the InChi string ... NCBO Seminar Series::Michel Dumontier

13. OpenBabel IUPAC 6-(hydroxymethyl)oxane-2,3,4,5-tetrol OR (2R,3R,4S,5R,6R)-6 -(hydroxymethyl)tetrahydro -2H-pyran-2,3,4,5-tetraol SMILES O1[C@@H]([C@@H](O)([C@H](O)([C@@H](O)([C@@H]1(O)))))(CO) 79025 InCHI InChI=1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1 SDF CML α-D-Glucose

14. OWL Has Explicit Semantics Can therefore be used to capture knowledge in a machine understandable way NCBO Seminar Series::Michel Dumontier

15. Chemical Ontology Chemical Knowledge for the Semantic Web.Mykola Konyk, Alexander De Leon, and Michel Dumontier. LNBI. 2008. 5109:169-176. Data Integration in the Life Sciences (DILS2008). Evry. France. 

16. http://code.google.com/p/semanticwebopenbabel/ NCBO Seminar Series::Michel Dumontier

17. Describing chemical functional groups in OWL-DL for the classification of chemical compounds methyl group hydroxyl group Ethanol Functional groups describe chemical reactivity in terms of atoms and their connectivity, and exhibits characteristic chemical behavior when present in a compound. Knowledge of functional groups is important in chemical synthesis, pharmaceutical design and lead optimization. N Villanueva-Rosales, MDumontier. 2007. OWLED, Innsbruck, Austria. NCBO Seminar Series::Michel Dumontier

18. Describing Functional Groups in DL HydroxylGroup: CarbonGroup that (hasSingleBondWith some (OxygenAtom that hasSingleBondWith some HydrogenAtom) R group O H R NCBO Seminar Series::Michel Dumontier

19. Fully Classified Ontology 35 FG NCBO Seminar Series::Michel Dumontier

20. And, we define certain compounds Alcohol: OrganicCompound that (hasPart some HydroxylGroup) NCBO Seminar Series::Michel Dumontier

21. Organic Compound Ontology 28 OC NCBO Seminar Series::Michel Dumontier

22. Question Answering Query PubChem, DrugBank and dbPedia* * Requires import of relevant URIs NCBO Seminar Series::Michel Dumontier

23. But... • Molecules represented as individuals because OWL-DL only allows tree-like class descriptions • No variable binding (e.g. ?x) ... no cyclic molecule/functional group descriptions at the class level  • Boris Motik et al has a proposal for Description Graphs, • Robert Stevens & Duncan Hull trying it out for chemical representation.... NCBO Seminar Series::Michel Dumontier

24. Identifiers for Atoms • Atom identifiers can be consistently retrieved from the OpenBabel model. • Canonical numbering means we can reliably refer to a specific region rather than a (possibly degenerate) sub-graph match. • In our plugin, URI component naming was based on the assigned molecule identifier e.g. pubchemid#aN, where N is the number • Use InChiKey as base? e.g. InChiKey#aN NCBO Seminar Series::Michel Dumontier

25. What about identifiers for collection of atoms? • Potentially useful in describing residues, PTMs, binding sites, etc. • Is the lack of connectivity sufficient? • Contiguous: • ranges (aN-aN) • enumerations (aN,aN,aN) • Non-contiguous: • Combination of ranges, enumerations? NCBO Seminar Series::Michel Dumontier

26. Can we reuse our positional nomenclature for residues? • Residues are generally referred to by their absolute position in the biopolymer sequence. e.g. Pro @ X on Protein Y InChiKey#a50-a65 owl:sameAs InChiKey#r5 InChiKey#r5_a1-r5_a15 owl:sameAs InChiKey#r5 • Collection of Residues might follow the same rules as a Collection of Atoms. • Useful for defining domains, motifs, etc NCBO Seminar Series::Michel Dumontier

27. An Alternative Scheme • We already have a simplified representation for biopolymers... • Canonical sequence is represented by a string of single letter characters • DNA: ACGT • RNA: ACGU • Proteins: 20 amino acids (not B,J,O,U,X,Z) • Modifications can be referred to with ChEBI/PSI-MOD ontology (e.g. Prolyl hydroxylated residue @ 402) • Each (modified) residue must have its InChi description so as to capture explicit structural deviations (de-protonation, etc) NCBO Seminar Series::Michel Dumontier

28. PSI-MOD contains modified residues with links to structural descriptions NCBO Seminar Series::Michel Dumontier

29. But what if we have a modification that isn’t contained in the ontology! • No problem... define your own term, with the corresponding structural description (InChi, SMILES), and add to an ontology document... • If you’re using OWL, you can add the import statement and publish it. • And, of course, you should submit it to the appropriate ontology development teams. (and later make it equivalent to) NCBO Seminar Series::Michel Dumontier

30. While we’re at it, we could extend our expressive capability to match that of OWL: • Specification • Exactly mod1@pos X • Only mod1@posX • Minimum : • At least mod1@posX • Combination: • mod1@posX AND mod2@posY, X != Y • Possibilities/Uncertainty: • (mod1 OR mod2) @posX • Exclusion: • not mod1 @ posX NCBO Seminar Series::Michel Dumontier

31. So what if... we describe the structural features of the molecule with OWL (sequence + PTMs), and generate an identifier from one of its serializations (RDF/XML?) that way we have the explicit description as the identifier in a form that is compatible with the semantic web. NCBO Seminar Series::Michel Dumontier

32. NCBO Seminar Series::Michel Dumontier

33. Uniprot example revisited :1 (HIF1α) :2 (HIF1α + P402hyd) :3 (HIF1α + P564hyd) :4 (HIF1α + P402hyd + P564hyd) :5 (EGLN1) :6 (VHL) :A rdfs:subClassOf :Hydroxylation :A hasParticipant (:0#r402 and :Substrate) :A hasParticipant (:1#r402 and :Product) :A hasParticipant (:5 and :Enzyme) :B rdfs:subClassOf :Interaction :B :hasParticipant (:2#r402 or :3#r564 or :4#r402,r564) :B :hasParticipant (:6) Please ignore the made up short-hand syntax! Under normoxic conditions, HIF1α is hydroxylated on Pro-402 and Pro-564 in the oxygen-dependent degradation domain (ODD) by EGLN1/PHD1 and EGLN2/PHD2. The hydroxylated prolines promote interaction with VHL, initiating rapid ubiquitination and subsequent proteasomal degradation . NCBO Seminar Series::Michel Dumontier

34. Infering Protein Participation :A rdfs:subClassOf :Hydroxylation :A hasParticipant (:0#r402 and :Substrate) :A hasParticipant (:1#r402 and :Product) :0#r402 :isPartOf :0 :1#r402 :isPartOf :1 :A hasParticipant :0 :A hasParticipant :1 • OWL Role Chain hasParticipant o isPartOf -> hasParticipant if process has the part as a participant, then the whole is also a participant NCBO Seminar Series::Michel Dumontier

35. Contextual, but non-structural considerations in identifier generation? • Chemical? • pH? • Temperature? • Environment (in vitro, in vivo, in silico)? • Biological? • Species? • mRNA/Gene from which it was transcribed/encoded? • Indirect Relationships? • Point & Multiple Mutations? • Alternative Splice Variants? • Sequence Similarity? NCBO Seminar Series::Michel Dumontier

36. Summary We need a precise method to generate identifiers for biopolymers and arbitrary sets of their parts. Consistent identifier generation will allow anybody to specify findings according to the biopolymers for which it was observed, whether it exists in a database or not, and will allow us to link biochemical knowledge at finer levels of granularity. (at least) two identifier schemes were put forward to initiate discussion, with the goal of setting a standard naming convention. NCBO Seminar Series::Michel Dumontier

37. dumontierlab.com michel_dumontier@carleton.ca Special thanks to PhD Student Leonid Chepelev for insightful discussions  semanticscience.org NCBO Seminar Series::Michel Dumontier