R/9_convert_metabolite_id.R
request_metabolite_id_systems.RdThis function returns the available metabolite identifier conversion systems supported by different online services, including **CTS FiehnLab**, **ChemSpider**, and **OpenAI**. It provides a list of identifier formats that can be used for conversion.
Character. The server to retrieve supported identifier formats from. Available options: - `"cts.fiehnlab"`: The **Chemical Translation Service (CTS) by FiehnLab** at UC Davis. - `"chemspider"`: The **ChemSpider API** provided by the Royal Society of Chemistry. - `"openai"`: Uses OpenAI's language models for metabolite ID conversions.
Character. Specifies whether to use a **local** or **online** source for fetching the available databases. Options: - `"local"`: Uses locally stored information about supported databases. - `"online"`: Fetches real-time data from the respective API endpoints.
A data frame or vector containing the supported **From-To** identifier conversions for the selected `server`. - If `server = "cts.fiehnlab"`, returns a vector of available **from** and **to** databases. - If `server = "chemspider"`, returns a data frame listing valid identifier conversions. - If `server = "openai"`, returns a predefined set of supported sources.
- **CTS FiehnLab**: The function queries `http://cts.fiehnlab.ucdavis.edu/rest/fromValues` to retrieve the list of supported database formats. - **ChemSpider**: Retrieves a predefined set of identifier conversions. - **OpenAI**: Returns a list of supported metabolite ID formats available through OpenAI models.
**ChemSpider API Key Requirement**: If using the `"chemspider"` server, an API key is required for querying ChemSpider’s services.
**How to Obtain a ChemSpider API Key:** 1. Visit the **Royal Society of Chemistry (RSC) Developer Portal**: [https://developer.rsc.org/](https://developer.rsc.org/) 2. Sign in or create an account. 3. Navigate to **My Account** > **API Keys**. 4. Apply for access to the **ChemSpider API**. 5. Once approved, generate your API key and copy it for use.
# Get supported conversion systems for CTS FiehnLab (local)
request_metabolite_id_systems(server = "cts.fiehnlab", source_format = "local")
#> [1] "AAA Chemistry"
#> [2] "ABBLIS Chemicals"
#> [3] "Abbott Labs"
#> [4] "ABI Chem"
#> [5] "AbMole Bioscience"
#> [6] "Acesobio"
#> [7] "Achemica"
#> [8] "Acorn PharmaTech"
#> [9] "Active Biopharma"
#> [10] "Adooq BioScience"
#> [11] "AK Scientific"
#> [12] "AKos Consulting & Solutions"
#> [13] "Alagar Yadav"
#> [14] "ALDRICH"
#> [15] "Alinda Chemical"
#> [16] "Alsachim"
#> [17] "Amadis Chemical"
#> [18] "Amatye"
#> [19] "Ambinter"
#> [20] "Ambit Biosciences"
#> [21] "AmicBase - Antimicrobial Activities"
#> [22] "Angene Chemical"
#> [23] "Angene International"
#> [24] "Anitha"
#> [25] "Annamalai Universtiy"
#> [26] "Annker Organics"
#> [27] "Anward"
#> [28] "Apeiron Synthesis"
#> [29] "ApexBio Technology"
#> [30] "Apexmol"
#> [31] "Ark Pharm"
#> [32] "Aromsyn catalogue"
#> [33] "Aronis"
#> [34] "ASINEX"
#> [35] "Aurora Fine Chemicals LLC"
#> [36] "Aurum Pharmatech LLC"
#> [37] "Avanti Polar Lipids"
#> [38] "Beijing Advanced Technology Co"
#> [39] "Bertin Pharma"
#> [40] "Bharathiar University"
#> [41] "Bharathidasan University"
#> [42] "Bhaskar Lab"
#> [43] "BIDD"
#> [44] "BIND"
#> [45] "BindingDB"
#> [46] "BioChemPartner"
#> [47] "BioCyc"
#> [48] "Biological Magnetic Resonance Data Bank (BMRB)"
#> [49] "Bioprocess Technology Lab"
#> [50] "Biosynth"
#> [51] "Broad Institute"
#> [52] "BroadPharm"
#> [53] "Burnham Center for Chemical Genomics"
#> [54] "Calbiochem"
#> [55] "Calicut University"
#> [56] "Cambridge Crystallographic Data Centre"
#> [57] "CAPOT"
#> [58] "CAS"
#> [59] "Cayman Chemical"
#> [60] "CC_PMLSC"
#> [61] "Center for Chemical Genomics"
#> [62] "ChEBI"
#> [63] "ChemBank"
#> [64] "Chembase.cn"
#> [65] "ChEMBL"
#> [66] "ChemBlock"
#> [67] "Chembo"
#> [68] "ChemBridge"
#> [69] "ChemDB"
#> [70] "ChemExper Chemical Directory"
#> [71] "ChemFrog"
#> [72] "Chemical Biology Department"
#> [73] "Chemical Name"
#> [74] "chemicalize.org by ChemAxon"
#> [75] "ChemIDplus"
#> [76] "ChemMol"
#> [77] "ChemScene"
#> [78] "ChemSpider"
#> [79] "ChemSynthesis"
#> [80] "ChemTik"
#> [81] "Chiralblock Biosciences"
#> [82] "Circadian Research"
#> [83] "CLRI (CSIR)"
#> [84] "CMLD-BU"
#> [85] "Columbia University Molecular Screening Center"
#> [86] "Comparative Toxicogenomics Database"
#> [87] "Creasyn Finechem"
#> [88] "Department of Bioinformatics"
#> [89] "Department of Biotechnology"
#> [90] "Department of Environmental Biotechnology"
#> [91] "Department of Microbiology"
#> [92] "Department of Pharmacy"
#> [93] "Department of Zoology"
#> [94] "DiscoveryGate"
#> [95] "DrugBank"
#> [96] "DTP/NCI"
#> [97] "EDASA Scientific Compounds June 2013"
#> [98] "EMD Biosciences"
#> [99] "Emory University Molecular Libraries Screening Center"
#> [100] "Enamine"
#> [101] "Ennopharm"
#> [102] "EPA DSSTox"
#> [103] "Excenen Pharmatech"
#> [104] "Exchemistry"
#> [105] "Faculty of Marine Sciences"
#> [106] "FINETECH"
#> [107] "Finley and King Labs"
#> [108] "FLUKA"
#> [109] "ForeChem"
#> [110] "Fragmenta"
#> [111] "Georganics"
#> [112] "GlaxoSmithKline (GSK)"
#> [113] "GLIDA"
#> [114] "GNF / Scripps Winzeler lab"
#> [115] "Golm Metabolome Database (GMD)"
#> [116] "GPCR-Ligand Database"
#> [117] "Hangzhou APIChem Technology"
#> [118] "Hangzhou Trylead Chemical Technology"
#> [119] "Harvard Medical School"
#> [120] "HDH Pharma"
#> [121] "Human Metabolome Database"
#> [122] "HUMGENEX"
#> [123] "IBCH RAS"
#> [124] "IBM"
#> [125] "ICCB-Longwood/NSRB Screening Facility"
#> [126] "IIT Guwahati"
#> [127] "Immunology Lab"
#> [128] "Inc."
#> [129] "Inc. (AKSCI)"
#> [130] "InChIKey"
#> [131] "InFarmatik"
#> [132] "Inhibitor 2"
#> [133] "Insect Molecular Biology Lab"
#> [134] "Ion Channels and Transporters"
#> [135] "IS Chemical Technology"
#> [136] "Isoprenoids"
#> [137] "iThemba Pharmaceuticals"
#> [138] "IUPHAR-DB"
#> [139] "Jamson Pharmachem Technology"
#> [140] "Japan Chemical Substance Dictionary (Nikkaji)"
#> [141] "Johns Hopkins Ion Channel Center"
#> [142] "Karpagam University"
#> [143] "Kay Laboratory"
#> [144] "KEGG"
#> [145] "Kingston Chemistry"
#> [146] "KUMGM"
#> [147] "LeadScope"
#> [148] "Leiden University Medical Center"
#> [149] "LipidMAPS"
#> [150] "LLC"
#> [151] "LMSD"
#> [152] "LMU"
#> [153] "Ltd"
#> [154] "M.Jeyam and G.Shalini. Biochematics Division"
#> [155] "Marine Medicinal Plant Biotechnology Laboratory"
#> [156] "Max Planck Institute of Molecular Physiology"
#> [157] "Max Planck Institute of Molecular Plant Physiology"
#> [158] "MedChemexpress MCE"
#> [159] "MIC Scientific"
#> [160] "MICAD"
#> [161] "Milwaukee Institute for Drug Discovery"
#> [162] "MLSMR"
#> [163] "MMDB"
#> [164] "Molecular Libraries Program"
#> [165] "MOLI"
#> [166] "MolPort"
#> [167] "MP Biomedicals"
#> [168] "MTDP"
#> [169] "Nanjing Pharmaceutical Factory"
#> [170] "Nantong Baihua Bio-Pharmaceutical Co."
#> [171] "National Cancer Institute (NCI)"
#> [172] "Nature Chemical Biology"
#> [173] "Nature Chemistry"
#> [174] "Nature Communications"
#> [175] "NCGC"
#> [176] "NIAID"
#> [177] "NIH Clinical Collection"
#> [178] "NINDS Approved Drug Screening Program"
#> [179] "NIST"
#> [180] "NIST Chemistry WebBook"
#> [181] "Nitric Oxide Research"
#> [182] "NMMLSC"
#> [183] "NMRShiftDB"
#> [184] "NovoSeek"
#> [185] "Oakwood Products"
#> [186] "ORST SMALL MOLECULE SCREENING CENTER"
#> [187] "P.Ravikumar"
#> [188] "P3 BioSystems"
#> [189] "PANACHE"
#> [190] "Paul Baures"
#> [191] "PCMD"
#> [192] "PDSP"
#> [193] "PENN-ABS"
#> [194] "PennChem-GAM"
#> [195] "PFC"
#> [196] "Phytomatics Laboratory"
#> [197] "priyadharshini sabarathinam angayarkanni murugesh palaniswamy"
#> [198] "Prous Science Drugs of the Future"
#> [199] "PubChem CID"
#> [200] "Pubchem SID"
#> [201] "Quorum sensing and Peptidomimetics Laboratory"
#> [202] "R.Sathishkumar"
#> [203] "R&D Chemicals"
#> [204] "Rangan Lab"
#> [205] "RSChem"
#> [206] "S.GURUDEEBAN"
#> [207] "SASTRA University"
#> [208] "SCRIPDB"
#> [209] "Selleck Chemicals"
#> [210] "Selleckbio"
#> [211] "SGCOxCompounds"
#> [212] "SGCStoCompounds"
#> [213] "Shanghai Institute of Organic Chemistry"
#> [214] "Shanghai Sinofluoro Scientific Company"
#> [215] "SIGMA"
#> [216] "Sigma-Aldrich"
#> [217] "SLING Consortium"
#> [218] "SMID"
#> [219] "SMILES"
#> [220] "Southern Research Institute"
#> [221] "Southern Research Specialized Biocontainment Screening Center"
#> [222] "Specialized Chemistry Center"
#> [223] "Specs"
#> [224] "Sri Venkateswara University"
#> [225] "SRMLSC"
#> [226] "Structural Genomics Consortium"
#> [227] "SureChem"
#> [228] "SYNCHEM OHG"
#> [229] "Syntechem"
#> [230] "T.RAMANATHAN & K.SATYAVANI"
#> [231] "TCI (Tokyo Chemical Industry)"
#> [232] "ten Dijke Lab"
#> [233] "Tetrahedron Scientific Inc"
#> [234] "The Scripps Research Institute Molecular Screening Center"
#> [235] "Therapeutic Targets Database"
#> [236] "Thomson Pharma"
#> [237] "TimTec"
#> [238] "Total TOSLab Building-Blocks"
#> [239] "Tox21"
#> [240] "True PharmaChem"
#> [241] "Tyger Scientific"
#> [242] "UCLA Molecular Screening Shared Resource"
#> [243] "UM-BBD"
#> [244] "UniCarbKB"
#> [245] "University of California at San Diego (UCSD)"
#> [246] "University of Kansas"
#> [247] "University of Michigan"
#> [248] "University of Pittsburgh Molecular Library Screening Center"
#> [249] "UPCMLD"
#> [250] "Vanderbilt Screening Center for GPCRs"
#> [251] "Vanderbilt Specialized Chemistry Center"
#> [252] "Vanderbilt University Medical Center"
#> [253] "VIT University"
#> [254] "Vitas-M Laboratory"
#> [255] "Watec Laboratories"
#> [256] "Watson International Ltd"
#> [257] "Web of Science"
#> [258] "xPharm"
#> [259] "Zancheng Functional Chemicals"
#> [260] "zealing chemical"
#> [261] "ZINC"