The supplement for "How large is the metabolome"
Kind T., Scholz M., Fiehn O. can be found under
http://fiehnlab.ucdavis.edu/projects/Rice_metabolome


Kind T, Scholz M, Fiehn O (2009) How Large Is the Metabolome? 
A Critical Analysis of Data Exchange Practices in Chemistry. 
PLoS ONE 4(5): e5440.; dx.doi.org/10.1371/journal.pone.0005440; 


Compounds were retrieved from 
http://www.ncbi.nlm.nih.gov/sites/batchentrez
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ZIP Archive contents:
1) readme.txt - this file
2) Plos-one-pub-known-CIDs.sdf - structures with known CIDs
3) bisbynin-correct.cml - Bisbinyn (not in PubChem)
4) bisbynin-correct.mol - Bisbinyn (not in PubChem) MOL connection table
5) plos-CIDs.txt - for BatchEntrez (select PubChem compounds)
6) rice-4-publication.ppt - 3 figures in PPT
7) *.tif - 3 figures as TIFF
8) rice-graphics.mrv - Figure 1 for the free ChemAxon Marvin View Editor
9) rice compounds - http://fiehnlab.ucdavis.edu/projects/Rice_metabolome/rice-target-list.zip

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Just for reference see
http://fiehnlab.ucdavis.edu/projects/Rice_metabolome


Programs:
1) TEXTPAD ($$) www.textpad.com
2) MS EXCEL ($$$) + Visual Basic www.microsoft.com
3) ChemAxon molconvert (free), cxcalc (academic license), JCHEM full (academic license)
4) ChemAxon Instant-JChem (free academic version)
5) EPA EPISuite (free)
6) Beilstein Crossfire for searching the Beilstein database of organic compounds and properties 
7) Scifinder Scholar for searching the CAS database
8) InChI and InChIkey software (free)

Databases and Services (updated):
1)  The PubChem database (free) - download the whole PubChem DB here: PubChem FTP
2)  The Dictionary of Natural Products ($$$$) Web version
3)  The KEGG database (free)
4)  The peptide DB and metabolome DB (free)
5)  The MDL Beilstein database ($$$$$)
6)  The CAS database ($$$$$ academic or $$$$$$ commercial)
7)  The ChemSpider DB (free) - largest information enhanced DB with mass spectrometry API
8)  The RiceCyc DB - Rice Metabolic Pathways: RiceCyc Home 
9)  The Reactome DB
10) The SetupX - biological experiment database
11) The KNApSAcK DB - Species-Metabolite Relationship Database
12) The SureChem patent database
13) The IBM Patent chemical search
14) The MetaCrop DB - a detailed database of crop plant metabolism
15) The LipidMaps DB - LIPID Metabolites And Pathways Strategy
16) The Dr. Duke's Phytochemical and Ethnobotanical Database
17) The NCBI Taxonomy DB
18) The Oryzabase - integrated rice sciences database
19) The IBM Chemical Patent search (Simple) beta
20) The BatchEntrez service to retrieve compounds from PubChem compound IDs
21) The InChiKey resolver from RSC and ChemSpider


Compound annotations from text (Name; PubChem CID; InChIKey):
2-acetyl-1-pyrroline; CID 522834; DQBQWWSFRPLIAX-UHFFFAOYAG
Vitamin-A; CID 445354; FPIPGXGPPPQFEQ-OVSJKPMPBW
Beta-carotene; CID 5280489; OENHQHLEOONYIE-JLTXGRSLBT
Bisbynin; CID NA; ICHJNTDKHBXTFN-CMZGOGIXBZ  [CML] [MOL] [ChemSpider]
Trans-luteine; CID 5368396; KBPHJBAIARWVSC-DKLMTRRABK
Cholesterol; CID 5997; HVYWMOMLDIMFJA-DPAQBDIFBB
Malathion; CID 4004; JXSJBGJIGXNWCI-UHFFFAOYAK
Chlorpyrifos; CID 2730; SBPBAQFWLVIOKP-UHFFFAOYAG
Ribosylnicotinamide; CID 439924; JLEBZPBDRKPWTD-ARWKKGFBBE
Omeprazol; CID 4594; SUBDBMMJDZJVOS-UHFFFAOYAZ
Rhodopinal; CID 20055178; GOJQFVQXKNNAAY-XQHLYSSHBM
Tegafur; CID 5386; WFWLQNSHRPWKFK-UHFFFAOYAE
Arginine; CID 232; ODKSFYDXXFIFQN-UHFFFAOYAT

Optical Character Recognition and Chemical Structure Recognition:
1) OSRA - Optical Structure Recognition (NIH) (free, open source)
2) Kekule - OCR-optical chemical (structure) recognition (NCI)
3) Clide -  Chemical literature data extraction tool (Univ. Leeds/ SimBioSys)
4) ChemoCR - Tool for Chemical Compound Reconstruction
5) ChemReader - Automated extraction of chemical structure information

Text based semantic annotation tools and projects:
1) Oscar3 - Open Source Chemistry Analysis Routines (open source)
2) Chem-MANTIS - Nomenclature Transformation Integrated System
3) Project Prospect - IUPAC, Ontology, CML, InChI enhanced chemical publications
4) Chemicalize.org - web based annotation service via ChemAxon proxy (name to structure)

Name to chemical structure converters (vice versa):
1) Autonom - Beilstein Institute
2) IBM Chemical Annotator - IBM Almaden
3) Lexichem - OpenEye
4) Struct <=> Name - CambridgeSoft
5) Marvin IUPAC Name - ChemAxon
6) ACDName - Structure to Name and  Name to Structure ACDLabs
7) NamExpert and Nomenclator - Cheminnovation
8) IUPAC NameIt - BioRad


