source/README-Extras

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

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