OPSIN Information

History

During the development of OSCAR the need to have a program to convert identified chemical names to connection tables arose. Due to the absence of any open source efforts with broad coverage of organic nomenclature work was started by Peter Murray-Rust and Joe Townsend on such a program. This work was continued by Peter Corbett cumulating in the creation of a system broadly similar to the current incarnation (Corbett and Murray-Rust 2006). In 2008 Daniel Lowe took over development of the project as part of his PhD during which time the range of nomenclature supported as been expanded substantially, along with improvements to the parser to cope with the complexity of the grammar of chemical names (Lowe et al. 2011). A comprehensive description of OPSIN, its algorithms and performance (as of mid 2012) is included in the PhD thesis (Lowe 2012). Development of OPSIN is still on-going with more nomenclature continuing to be added (Lowe et al. 2013).

Examples of Supported Nomenclature

Nomenclature	Examples
Alk/ane/ene/yne	hexane hex-1-ene hex-1-yne
Heteroatom chains	tetrasilane tetrasiloxane
Cyclised chains	cyclohexane cyclotriborazane
Trivial acids and derivatives	maleic acid maleamic acid maleamide maleimide
Hantzsch-Widman rings	1,3-oxazole
Spiro compounds	spiro[4.5]decane pentaspiro[2.0.24.1.1.210.0.213.18.23]octadecane 1H,1'H-2,2'-spirobi[naphthalene] 2λ6,2',2''-spiroter[[1,3,2]benzodioxathiole] 1'H,1''H,2H,8'H-1,2':7',2''-dispiroter[naphthalen]-1'-one spiro[1,2-benzodithiole-3,2'-[1,3]benzodithiole]
von Baeyer systems	pentacyclo[13.7.4.33,8.018,20.113,28]triacontane
Hydro/dehydro	2,3-dihydropyridine 1,2-didehydrobenzene
Indicated hydrogen	1H-benzoimidazole phosphinin-2(1H)-one
Heteroatom replacement	3-aza-pentane 3-azonia-pentane 3-azanylia-pentane 3-azanida-pentane 3-azanuida-pentane
Specification of charge: ium/ide/ylium/uide	azanium boranuide
Multiplicative nomenclature	ethylenediaminetetraacetic acid 3,3'-[ethane-1,2-diylbis(oxy)]bis{4-[2-(furan-3-yloxy)ethoxy]furan}
Conjunctive nomenclature	1,3,5-benzenetriacetic acid
Fused ring systems	imidazo[4,5-d]pyridine phenothiazino[3',4':5,6][1,4]oxazino[2,3-i]benzo[5,6][1,4]thiazino[3,2-c]phenoxazine phenanthro[4,5-bcd:1,2-c']difuran
Simple bridges	2,3-methanoindene 3,4-methylenedioxy-β-methoxyphenethylamine 3,4-epoxy-3,4-dihydrophenanthrene
Ring assemblies	biphenyl 2,2':6',2''-terpyridine
Prefix functional replacement	peroxybenzoic acid
Infix functional replacement	benzoperoxoic acid
Lambda convention	λ5-phosphane
Perhalogenation	perchloro-3,4-dimethylenecyclobutene
Radicofunctional nomenclature	acetals, acids, alcohols, amides, anhydrides, anilides, azetidides, azides, bromides, chlorides, cyanates, cyanides, esters, di/tri/tetra esters, ethers, fluorides, fulminates, glycol ethers, glycols, hemiacetals, hemiketal, hydrazides, hydrazones, hydrides, hydroperoxides, hydroxides, imides, iodides, isocyanates, isocyanides, isoselenocyanates, isothiocyanates, ketals, ketones, lactams, lactims, lactones, mercaptans, morpholides, oxides, oximes, peroxides, piperazides, piperidides, pyrrolidides, selenides, selenocyanates, selenoketones, selenolsselenosemicarbazones, selenones, selenoxides, selones, semicarbazones, sulfides, sulfones, sulfoxides, sultams, sultims, sultines, sultones, tellurides, telluroketones, tellurones, tellurosemicarbazones, telluroxides, thiocyanates, thioketones, thiols and thiosemicarbazones
Amino Acids and derivatives	glycinol L-2-aminobutyric acid L-alanyl-L-glutaminyl-L-arginyl-O-phosphono-L-seryl-L-alanyl-L-proline
Nucleosides, nucleotides and their esters	adenosine 5'-(tetrahydrogen triphosphate)
Steroids including alpha/beta stereochemistry	(3β)-cholest-5-en-3-ol
Open-chain monosaccharides	4-amino-4,6-dideoxy-3-C-methyl-2-O-methyl-L-mannose
Cyclised monosaccharides and glycosides	β-D-ribofuranose β-D-fructofuranosyl α-D-glucopyranosyl-(1->4)-α-D-glucopyranoside
Deoxy and anhydro	5-acetamido-2,7-anhydro-3,5-dideoxy-D-glycero-α-D-galacto-non-2-ulopyranosonic acid
Basic inorganic support	aluminium(3+) chloride mercury(II) chloride
Isotope specification	(2H6)propan-2-one acetone-d6 hexadeuterioacetone
R/S stereochemistry	(1R,3S)-3-amino-3-methylcyclohexanecarboxylic acid
E/Z stereochemistry	(2Z)-but-2-ene
cis/trans indicating relative stereochemistry on rings	cis-1,4-dimethylcyclohexane
Structure-based polymer names	poly(2,2'-diamino-5-hexadecylbiphenyl-3,3'-diyl)

References

[1] Peter Corbett and Peter Murray-Rust. High-Throughput Identification of Chemistry in Life Science Texts. Lecture Notes in Computer Science. 2006, 4216, pp107-118. DOI: 10.1007/11875741_11

[2] Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen. Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling. 2011, 51 (3), 739-753 DOI: 10.1021/ci100384d

[3] Daniel M. Lowe. Extraction of chemical structures and reactions from the literature. Ph.D. Thesis, University of Cambridge, 2012. Available from Apollo.

[4] Daniel M. Lowe, Peter Murray-Rust, Robert C. Glen. OPSIN: Taming the Jungle of IUPAC Chemical Nomenclature. 6th Joint Sheffield Conference on Chemoinformatics, 2013. Available from here.

Libraries

OPSIN utilises dk.brics.automaton to provide a discrete finite state automaton to allow the parsing of chemical names. Woodstox is used as an XML framework for reading in resource files and writing CML. JNI-InChI is used to generate InChIs. Additionally for testing JUnit and Mockito are employed. The web interface is powered by Restlet with the Indigo toolkit being used for 2D coordinate generation and depiction.

OPSIN's developers use YourKit to profile and optimise code.

YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications.

License and Warranty

OPSIN is licensed under the MIT License

OPSIN is made available in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.