README-Extras: auxiliary information files for PubChem These files contain data present in PubChem but not part of the individual structure records. Each file is regenerated in full with every full or incremental dump, and so will always correspond to the most current state of the database. MD5 checksums are present for each file. CID-MeSH: This file contains associations between CID and MeSH terms. The format is a simple text file where each line has an id, followed by one or more MeSH terms associated with that id, separated by tab characters. Note that each term may contain multiple words separated by spaces. MeSH-Pharm: This is a mapping from MeSH terms to the pharmacological action(s) assigned to each term (by MeSH), for each term used in the PubChem Compound database; it is thus only a subset of all MeSH terms. Along with the aforementioned CID-MeSH files, this allows one to map CID to pharmacological actions. The format is a simple text file where each line has a MeSH term followed by one or more pharmacological actions associated with that term, separated by tabs. Note that both terms and pharmacological actions may themselves have more than one word, separated by spaces. Source-Names: PubChem Depositors have both a "Data Source ID" - which for newer depositors is a numeric identifier but for older depositors is a text name; and a "Display Name" - which is the name shown on the depositor's substance summaries. There may be more than one display name, and the most recent one is what is shown. However, the substance blobs stored on this FTP site or downloaded live contain only the depositor source id in the attribution. This file maps source id to display name, and lists on each line (separated by tabs) the depositor source id, the corresponding display name, and the date when that display name was added. If the source id and display name are the same (mainly for older depositors), they are not listed in this file. CID-SID.gz: This is a mapping of CID to SID(s) from which each CID is derived. It is a gzipped text file where each line has CID, the SID it is linked to, and the type, all separated by tabs. The type is an integer that indicates the relationship of the CID to that SID: 1 Standardized Form of the Deposited Substance (all atoms) 2 Component of the Standardized Form (compoonents may be neutralized) CID-Component.gz: This is a mapping of CID to its component CID(s). It is a gzipped text file where each line has a CID, followed by a tab-separated list of component CIDs. Note that if there is only a single component, it will be the neutralized form. If there are multiple components, they are the (neutralized) separate covalent units. CID-Synonym-filtered.gz: CID-Synonym-unfiltered.gz: These are listings of all names associated with a CID. The unfiltered list are names aggregated from all SIDs whose standardized form is that CID, sorted by weight with the "best" names first. The filtered list has some names removed that are considered inconsistent with the structure. Both are gzipped text files with CID, tab, and name on each line. Note that the names may be composed of more than one word, separated by spaces. CID-Parent.gz: This is a listing of all CIDs with parents. It is a gzipped text file with CID, tab, and parent on each line. Note that a CID may be a parent of itself, or may have no parent. CID-InChI-Key.gz: This is a listing of all CIDs with their full InChI strings and InChI keys. It is a gzipped text file with CID, tab, InChI, tab, InChI Key on each line. CID-SMILES.gz: This is a listing of all CIDs with their isomeric SMILES. It is a gzipped text file with CID, tab, SMILES on each line. CID-IUPAC.gz: This is a listing of all CIDs with their computed IUPAC names. It is a gzipped text file with CID, tab, IUPAC on each line. Note that the names may contain UTF8 characters. CID-Title.gz: This is a listing of all CIDs with the name chosen as title for the respective compound summary page. It is a gzipped text file with CID, tab, title on each line. CID-Date.gz: This is a listing of all (live) CIDs with their creation date - the date when that CID first appeared in PubChem. It is a gzipped text file with CID, tab, and date (YYYY-MM-DD) on each line. CID-LCSS.xml.gz: This is an XML file containing the compound summary data for all LCSS records within the PubChem Compound database. CID-Patent.gz: This is a listing of all patent documents linked to CIDs. These are in Google's "publication number" format, following PubChem's matching of depositor-supplied patent identifiers to publication numbers. It is a gzipped text file with CID, tab, and publication number on each line. CID-PMID.gz: This is a listing of all PubMed IDs (PMIDs) linked to CIDs. It is a gzipped text file with CID, tab, PMID, tab, and type on each line. The types are: 1 PMIDs provided by PubChem Substance depositors 2 PMIDs from the MeSH heading(s) linked to the given CID 3 PMIDs provided by PubMed publishers 4 PMIDs associated through BioAssays CID-Mass.gz: This is a listing of all CIDs with their molecular formulas and monoisotopic and exact masses. It is a gzipped text file with CID, tab, formula, tab, monoisotopic mass, tab, exact mass on each line. CID-Identifiers.gz: This is a listing of all CIDs with their third-party database identifiers. It is a gzipped text file with CID, tab, identifier, tab, identifier type on each line. SID-Date.gz: This is a listing of all (live) SIDs with their creation and modification dates - the date when that SID first appeared in PubChem, and the date when it was last modified (to bring it to the current version). It is a gzipped text file with SID, tab, creation date (YYYY-MM-DD), tab, and modification date on each line. SID-Map.gz: This is a listing of all (live) SIDs with their source names and registry identifiers, and the standardized CID if present. It is a gzipped text file where each line contains at least three columns: SID, tab, source name, tab, registry identifier; then a fourth column of tab, CID if there is a standardized CID for the given SID. SID-Synonym.gz: This is a listing of all (live) SIDs with their depositor provided synonyms (one per line). It is a gzipped text file with SID, tab, synonym on each line. CID-Preferred.gz: This is a listing of CIDs that are no longer live, and that have a new "preferred" form as a result of restandardization of the PubChem database. It is a gzipped text file with old CID, tab, and new preferred CID on each line. PubChem-Reference-Collection.tsv.gz: This is a dump of PubChem Reference Collection Records. It contains multiple columns separated by tab, e.g. SID, RefChemID, PreferredName, Synonyms, PreferredCID, OtherCIDs, PreferredInChIKey, OtherInChIKeys, Related, CreateDate, ModifyDate, etc. If there are multiple records in a column, "|" is used to separated them. The Related column contains a list of related records and their relationships in the format of "relation:PreferredName". For records that don't have a discrete structure, the PreferredCID is 0. Drug-Names.tsv.gz: This file contains drug synonyms, drug names, PubChem CIDs and their corresponding PubChem URLs. A "drug" in this context refers to any records identified as an active ingredient in drug labels published on NLM's DailMed Web site. CID-Biologics.tsv.gz: This file contains biologic line notations generated by NextMove's Sugar & Splice software. It is a gzipped text file with CID, tab, type, tab, and notation on each line. Note that a given CID may not have all types of notations. The types are: 1: IUPAC Condensed 2: LINUCS 3: Sequence 4: PLN 5: HELM 6: IUPAC :-= Fair Use Disclaimer =-: Databases of molecular data on the NCBI FTP site include such examples as nucleotide sequences (GenBank), protein sequences, macromolecular structures, molecular variation, gene expression, and mapping data. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein. However, some submitters of the original data may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims and, therefore, cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases.