PubChem Indice, Links and Filters removed in October 2016
PubChem Compound Indice removed

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ActiveAid [AA]: Active BioAssay identifier, integer. This choice is intended for users querying for active compounds for a particular assay. BioAssay ID (AID) should be provided.
ActiveConcentration: Using this filter users can query for compounds which show certain extent of active concentration(uM) in biological assays.
AssaySourceName [ASRC, ASRCNAM, ASRCNAME]: Allows filtering of by assay source name. For available data sources look here
BioAssayID [BAID, AID]: BioAssay identifier, integer.
InactiveAid [IA]: Inactive BioAssay identifier, integer. This choice is intended for users querying for inactive compounds for a particular assay. BioAssay ID (AID) should be provided.
InactiveAidCount [IC, ICNT]: Using this filter users can query for compounds which are inactive in a certain number of assays
MeSHDescription [MHD]
MeSHTreeNode [MSHN, MESHTN]: Medical Subject Heading tree node (tree structures). Searching for a term corresponding to a higher level node in the MeSH hierarchy will find records matching any MeSH terms beneath that node. For example, "Penicillins[MeSHTreeNode]" will find records linked to MeSH terms "Oxacillin", "Cloxacillin", etc. Note that entry terms (synonyms) for MeSH tree nodes are also indexed.
SourceID [SRID, SRCID]: Depositor's external id.
TautomerCount [TC, TCNT, TTMC]: Possible tautomer count for each given structure, no more than 200, integer. 
TestedConcentration : Using this filter users can query for compounds which are tested under certain concentrations(uM) in biological assays.
PubChem Substance Indice removed

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ActiveAid [AA]: Active BioAssay identifier, integer. This choice is intended for users querying for active substances for a particular assay.
ActiveAidCount [AC, ACNT]: Using this filter users can query for compounds which are active in a certain number of assays.
ActiveAidRatio [AAR]: Ratio should be between zero and 1. Ratio equals to the number of BioAssays where substances were tested active divided by number of BioAssays where substances tested with any result.
ActiveConcentration: Using this filter users can query for substances which show certain extent of active concentration(uM) in biological assays.
AtomChiralCount [ACC, ACCNT]: Total count of chiral atoms in a given compound, integer.
AtomChiralDefCount [ACDC, ACDCNT] --  Total count of defined chiral atoms in a given compound, integer.
AtomChiralUndefCount [ACUC, ACUCNT] --  Total count of undefined chiral atoms in a given compound, integer.
BioAssayID [BAID, AID]: BioAssay identifier, integer.
BondChiralCount [BCC, BCCNT]: Total count of chiral bonds in a given compound, integer.
BondChiralDefCount [BCDC, BCDCNT]: Total count of defined chiral bonds in a given compound, integer.
BondChiralUndefCount [BCUC, BCUCNT]: Total count of undefined chiral bonds in a given compound, integer.
Complexity [CPLX]: Substance structure complexity.
CovalentUnitCount [CUC, CUCNT]: Integer.
Element [ELMT, EL]: Chemical element in a substance/compound.
ExactMass [EMAS, EXMASS]-- The calculated mass of an ion or a molecule containing most likely isotopic composition for a single random molecule, corresponding to mass of most intense ion/molecule peak in a MS spec. A real number.
HeavyAtomCount [HAC, HACNT]: Atom count in a compound except hydrogen, integer.
HydrogenBondAcceptorCount [HBAC, HBACNT]: Hydrogen bond acceptors for a compound, integer.
HydrogenBondDonorCount [HBDC, HBDCNT]: Hydrogen bond donors for a compound, integer.
InactiveAid [IA]: Inactive BioAssay identifier, integer. This choice is intended for users querying for inactive substances for a particular assay. BioAssay ID (AID) should be provided.
InactiveAidCount [IC, ICNT]: Using this filter users can query for substances which are inactive in a certain number of assays
InChI [inch, inchi]: Standard IUPAC International Chemical Identifier. More info..
InChIKey [INCHIKEY]: Standard IUPAC International Chemical Identifier Key.
IsotopeAtomCount [IAC, IACNT]: Isotope atom numbers in a compound.
IUPACName [UPAC, IUPAC]: Standard IUPAC name for compound.
MeSHDescription [MHD]
MeSHTerm [MSHT, MESHT]: Medical Subject Heading term. Note that MeSH entry terms (synonyms for the Medical Subject Heading term) are also indexed.
MeSHTreeNode [MSHN, MESHTN]: Medical Subject Heading tree node (tree structures). Searching for a term corresponding to a higher level node in the MeSH hierarchy will find records matching any MeSH terms beneath that node. For example, "Penicillins[MeSHTreeNode]" will find records linked to MeSH terms "Oxacillin", "Cloxacillin", etc. Note that entry terms (synonyms) for MeSH tree nodes are also indexed.
MolecularWeight [MW, MWT, MOLWT]: Mass of a molecule calculated using the average mass of each element weighted for its natural isotopic abundance. E.g., Carbon has two natural isotopes 12 and 13 with relative abundances of 98.9% and 1.1% to yield an average mass of 12.011 g/mol. A real number.
MonoisotopicMass [MMAS, MIMASS]: Mass of a molecule calculated using the mass of the most abundant isotope of each element. E.g., Carbon has a monoisotopic mass of 12.000 g/mol. A real number.
PharmAction [PHMA, PHARMA]: MeSH pharmacological actions.
RotatableBondCount [RBC, RBCNT]: Count of rotatable bonds
TautomerCount [TC, TCNT, TTMC]: Possible tautomer count for each given structure, no more than 200, integer. 
TestedConcentration : Using this filter users can query for substances which are tested under certain concentrations(uM) in biological assays.
TotalFormalCharge [TFC, CHG, CHRG]: Total formula charge.
TPSA [TPSA]: Topological Polar Surface Area.
XLogP [XLGP, LOGP]
PubChem BioAssay Indice removed

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ActiveCidCount [ACC, ACCNT]: Number of unique chemicals (identified by CID--compound identifiers from Pccompound) that are considered as active in a BioAssay.
CompoundIDActive [CIDA]: CID(compound identifier from Pccompound) of a chemical that is considered as active in a BioAssay.
CompoundIDTested [CIDT]: CID(compound identifier from Pccompound) of a chemical that is tested in a BioAssay.
InactiveCidCount [IACC, IACCNT]: Number of unique chemicals (identified by CID--compound identifiers from Pccompound) that are considered as inactive in a BioAssay.
InactiveSidCount [IAC, IACNT]: Number of substances (identified by SID--substance identifier from Pcsubstance) that are considered as inactive in a BioAssay.
InconclusiveCidCount [ICC, ICCNT]: Number of unique chemicals (identified by CID--compound identifiers from Pccompound) that are considered as inconclusive regarding to be active or inactive in a BioAssay.
InconclusiveSidCount [IC, ICNT]: Number of substances (identified by SID--substance identifier from Pcsubstance) that are considered as inconclusive regarding to be active or inactive in a BioAssay.
MeSHDescriptionActive MHDA]: Medical Subject Heading descriptions that are associated with an active chemical structure in a BioAssay.
MeSHDescriptionTested [MHDT]: Medical Subject Heading descriptions that are associated with any chemical structure tested in a BioAssay.
MeSHTermActive [MHTA]: Medical Subject Heading terms that are only associated with an active chemical structure in a BioAssay.
MeSHTermTested [MHTT]: Medical Subject Heading terms that are associated with any chemical structure tested in a BioAssay.
PharmActionActive [PHAA]: MeSH pharmacological actions that are associated with an active chemical structure in a assay.
PharmActionTested [PHAT]: MeSH pharmacological actions that are associated with an any chemical structure tested in a assay.
ReadoutCount [RC, RCNT]: Number of total test result fields(readouts) in a BioAssay
SubstanceIDActive [SIDA]: SID(substance identifier from Pcsubstance) of a substance that is considered as active in a BioAssay.
SubstanceIDTested [SIDT]: SID(substance identifier from Pcsubstance) of a substance that is tested in a BioAssay.
SynonymActive [SYNA]: MESH names and synonyms that are associated only with an active chemical structure in a BioAssay.
TestedConcentration : Using this filter users can query for assays where substances are tested in certain concentration(uM).
TidDescription [TDES, TIDD, TDESC, TDSC]: Description of a test result field in a BioAssay
TidName [TNAM, TIDN, TNAME]: Name of a test result field in a BioAssay
TotalCidCount [TCC]: Total number of unique chemicals (identified by CID--compound identifiers from Pccompound) that are tested in a BioAssay.
XRefAid [XRAD]: NCBI Entrez PubChem BioAssays identifier.
XRefAsurl [XRAL]: URL of the BioAssay provided by depositor.
XRefComment [XRCT]
XRefDburl [XRDL]: URL of Depositor's organization.
XRefGene [XRGN]: NCBI Entrez Gene identifier referred by a BioAssay.
XRefGi [XRGI]: NCBI Entrez Protein/Nucleotide GI number referred by a BioAssay.
XRefMmdb [XRMB]: NCBI Entrez Molecular Modeling Database(MMDB) identifiers(MMDB ID) referred by a BioAssay.
XRefNucleotidegi [XRefNCGI, XRNI]: NCBI Entrez Nucleotide identifier referred by a BioAssay.
XRefOmim [XRMM]: NCBI Entrez OMIM identifier.
XRefPmid [XRPD]: NCBI Entrez PubMed identifiers(PubMed ID) referred by a BioAssay.
XRefProteingi [XRefPRGI, XRPI]: NCBI Entrez Protein identifier referred by a BioAssay.
XRefSburl [XRSL]
XRefTaxonomy [XRTY]: NCBI Entrez Taxonomy identifier.
PubChem Compound Links removed

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pccompound_pcassay_inconclusive
pccompound_pcassay_panel_active
pccompound_pcassay_panel_inactive
pccompound_probe
PubChem Substance Links removed

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pcsubstance_mesh
pcsubstance_pcassay_inconclusive
pcsubstance_pcassay_panel_active
pcsubstance_pcassay_panel_inactive
pcsubstance_pcsubstance_parent_connectivity_pulldo
pcsubstance_pcsubstance_parent_isotopes_pulldown
pcsubstance_pcsubstance_parent_pulldown
pcsubstance_pcsubstance_parent_stereo_pulldown
pcsubstance_pcsubstance_parent_tautomer_pulldown
pcsubstance_pcsubstance_same_pulldown
pcsubstance_pcsubstance_sameanytautomer_pulldown
pcsubstance_pcsubstance_sameconnectivity_pulldow
pcsubstance_pcsubstance_sameisotopic_pulldown
pcsubstance_pcsubstance_samestereochem_pulldown
pcsubstance_pubmed_mesh
PubChem BioAssay Links removed

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pcassay_biosystems_active
pcassay_biosystems_target
pcassay_gene
pcassay_pcassay_biosystemsneighbor_list
pcassay_pccompound_inconclusive
pcassay_pccompound_panel_active
pcassay_pccompound_panel_inactive
pcassay_pcsubstance_inconclusive
pcassay_pcsubstance_panel_active
pcassay_pcsubstance_panel_inactive
pcassay_protein
pcassay_protein_target_pig
PubChem Substance Filters removed

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has_3d_conformer: records have 3d conformers
has_dailymed: records with associated dailymed info
has_mesh: records with associated MeSH terms
has_no_parent: records that do not have a parent
has_parent: records that have a parent structure
has_pharm: records with associated pharmacological actions