How to store data like Freebase does?

Question

I admit that this is basically a duplicate question of Use freebase data on local server? but I need more detailed answers than have already been given there

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Answer 1

This is what worked for me. It allows you to load all of a Freebase dump in a standard MySQL installation on less than 100GB of disk. The key is understanding the data layout in a dump and then transforming it (optimizing it for space and speed).

Freebase notions you should understand before you attempt to use this (all taken from the documentation):

• Topic - anything of type '/common/topic', pay attention to the different types of ids you may encounter in Freebase - 'id', 'mid', 'guid', 'webid', etc.
• Domain
• Type - 'is a' relationship
• Properties - 'has a' relationship
• Schema
• Namespace
• Key - human readable in the '/en' namespace

Some other important Freebase specifics:

• the query editor is your friend
• understand the 'source', 'property', 'destination' and 'value' notions described here
• everything has a mid, even things like '/', '/m', '/en', '/lang', '/m/0bnqs_5', etc.; Test using the query editor: [{'id':'/','mid':null}]​
• you don't know what any entity (i.e. row) in the data dump is, you have to get to its types to do that (for instance how do I know '/m/0cwtm' is a human);
• every entity has at least one type (but usually many more)
• every entity has at least one id/key (but usually many more)
• the ontology (i.e. metadata) is embedded in the same dump and the same format as the data (not the case with other distributions like DBPedia, etc.)
• the 'destination' column in the dump is the confusing one, it may contain a mid or a key (see how the transforms bellow deal with this)
• the domains, types, properties are namespace levels at the same time (whoever came up with this is a genius IMHO);
• understand what is a Topic and what is not a Topic (absolutely crucial), for example this entity '/m/03lmb2f' of type '/film/performance' is NOT a Topic (I choose to think of these as what Blank Nodes in RDF are although this may not be philosophically accurate), while '/m/04y78wb' of type '/film/director' (among others) is;

Transforms

(see the Python code at the bottom)

TRANSFORM 1 (from shell, split links from namespaces ignoring notable_for and non /lang/en text):

python parse.py freebase.tsv  #end up with freebase_links.tsv and freebase_ns.tsv

TRANSFORM 2 (from Python console, split freebase_ns.tsv on freebase_ns_types.tsv, freebase_ns_props.tsv plus 15 others which we ignore for now)

import e
e.split_external_keys( 'freebase_ns.tsv' )

TRANSFORM 3 (from Python console, convert property and destination to mids)

import e
ns = e.get_namespaced_data( 'freebase_ns_types.tsv' )
e.replace_property_and_destination_with_mid( 'freebase_links.tsv', ns )    #produces freebase_links_pdmids.tsv
e.replace_property_with_mid( 'freebase_ns_props.tsv', ns ) #produces freebase_ns_props_pmids.tsv

TRANSFORM 4 (from MySQL console, load freebase_links_mids.tsv, freebase_ns_props_mids.tsv and freebase_ns_types.tsv in DB):

CREATE TABLE links(
source      VARCHAR(20), 
property    VARCHAR(20), 
destination VARCHAR(20), 
value       VARCHAR(1)
) ENGINE=MyISAM CHARACTER SET utf8;

CREATE TABLE ns(
source      VARCHAR(20), 
property    VARCHAR(20), 
destination VARCHAR(40), 
value       VARCHAR(255)
) ENGINE=MyISAM CHARACTER SET utf8;

CREATE TABLE types(
source      VARCHAR(20), 
property    VARCHAR(40), 
destination VARCHAR(40), 
value       VARCHAR(40)
) ENGINE=MyISAM CHARACTER SET utf8;

LOAD DATA LOCAL INFILE "/data/freebase_links_pdmids.tsv" INTO TABLE links FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE "/data/freebase_ns_props_pmids.tsv" INTO TABLE ns FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE "/data/freebase_ns_base_plus_types.tsv" INTO TABLE types FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

CREATE INDEX links_source            ON links (source)             USING BTREE;
CREATE INDEX ns_source               ON ns    (source)             USING BTREE;
CREATE INDEX ns_value                ON ns    (value)              USING BTREE;
CREATE INDEX types_source            ON types (source)             USING BTREE;
CREATE INDEX types_destination_value ON types (destination, value) USING BTREE;

Code

Save this as e.py:

import sys

#returns a dict to be used by mid(...), replace_property_and_destination_with_mid(...) bellow
def get_namespaced_data( file_name ):
    f = open( file_name )
    result = {}

    for line in f:
        elements = line[:-1].split('\t')

        if len( elements ) < 4:
            print 'Skip...'
            continue

        result[(elements[2], elements[3])] = elements[0]

    return result

#runs out of memory
def load_links( file_name ):
    f = open( file_name )
    result = {}

    for line in f:
        if len( result ) % 1000000 == 0:
            print len(result)
        elements = line[:-1].split('\t')
        src, prop, dest = elements[0], elements[1], elements[2]
        if result.get( src, False ):
            if result[ src ].get( prop, False ):
                result[ src ][ prop ].append( dest )
            else:
                result[ src ][ prop ] = [dest]
        else:
            result[ src ] = dict([( prop, [dest] )])

    return result

#same as load_links but for the namespaced data
def load_ns( file_name ):
    f = open( file_name )
    result = {}

    for line in f:
        if len( result ) % 1000000 == 0:
            print len(result)
        elements = line[:-1].split('\t')
        src, prop, value = elements[0], elements[1], elements[3]
        if result.get( src, False ):
            if result[ src ].get( prop, False ):
                result[ src ][ prop ].append( value )
            else:
                result[ src ][ prop ] = [value]
        else:
            result[ src ] = dict([( prop, [value] )])

    return result

def links_in_set( file_name ):
    f = open( file_name )
    result = set()

    for line in f:
        elements = line[:-1].split('\t')
        result.add( elements[0] )
    return result

def mid( key, ns ):
    if key == '':
        return False
    elif key == '/':
        key = '/boot/root_namespace'
    parts = key.split('/')
    if len(parts) == 1:           #cover the case of something which doesn't start with '/'
        print key
        return False
    if parts[1] == 'm':           #already a mid
        return key
    namespace = '/'.join(parts[:-1])
    key = parts[-1]
    return ns.get( (namespace, key), False )

def replace_property_and_destination_with_mid( file_name, ns ):
    fn = file_name.split('.')[0]
    f = open( file_name )
    f_out_mids = open(fn+'_pdmids'+'.tsv', 'w')

    def convert_to_mid_if_possible( value ):
        m = mid( value, ns )
        if m: return m
        else: return None

    counter = 0

    for line in f:
        elements = line[:-1].split('\t')
        md   = convert_to_mid_if_possible(elements[1])
        dest = convert_to_mid_if_possible(elements[2])
        if md and dest:
            elements[1] = md
            elements[2] = dest
            f_out_mids.write( '\t'.join(elements)+'\n' )
        else:
            counter += 1

    print 'Skipped: ' + str( counter )

def replace_property_with_mid( file_name, ns ):
    fn = file_name.split('.')[0]
    f = open( file_name )
    f_out_mids = open(fn+'_pmids'+'.tsv', 'w')

    def convert_to_mid_if_possible( value ):
        m = mid( value, ns )
        if m: return m
        else: return None

    for line in f:
        elements = line[:-1].split('\t')
        md = convert_to_mid_if_possible(elements[1])
        if md:
            elements[1]=md
            f_out_mids.write( '\t'.join(elements)+'\n' )
        else:
            #print 'Skipping ' + elements[1]
            pass

#cPickle
#ns=e.get_namespaced_data('freebase_2.tsv')
#import cPickle
#cPickle.dump( ns, open('ttt.dump','wb'), protocol=2 )
#ns=cPickle.load( open('ttt.dump','rb') )

#fn='/m/0'
#n=fn.split('/')[2]
#dir = n[:-1]


def is_mid( value ):
    parts = value.split('/')
    if len(parts) == 1:   #it doesn't start with '/'
        return False
    if parts[1] == 'm':
        return True
    return False

def check_if_property_or_destination_are_mid( file_name ):
    f = open( file_name )

    for line in f:
        elements = line[:-1].split('\t')
        #if is_mid( elements[1] ) or is_mid( elements[2] ):
        if is_mid( elements[1] ):
            print line

#
def split_external_keys( file_name ):
    fn = file_name.split('.')[0]
    f = open( file_name )
    f_out_extkeys  = open(fn+'_extkeys' + '.tsv', 'w')
    f_out_intkeys  = open(fn+'_intkeys' + '.tsv', 'w')
    f_out_props    = open(fn+'_props'   + '.tsv', 'w')
    f_out_types    = open(fn+'_types'   + '.tsv', 'w')
    f_out_m        = open(fn+'_m'       + '.tsv', 'w')
    f_out_src      = open(fn+'_src'     + '.tsv', 'w')
    f_out_usr      = open(fn+'_usr'     + '.tsv', 'w')
    f_out_base     = open(fn+'_base'    + '.tsv', 'w')
    f_out_blg      = open(fn+'_blg'     + '.tsv', 'w')
    f_out_bus      = open(fn+'_bus'     + '.tsv', 'w')
    f_out_soft     = open(fn+'_soft'    + '.tsv', 'w')
    f_out_uri      = open(fn+'_uri'     + '.tsv', 'w')
    f_out_quot     = open(fn+'_quot'    + '.tsv', 'w')
    f_out_frb      = open(fn+'_frb'     + '.tsv', 'w')
    f_out_tag      = open(fn+'_tag'     + '.tsv', 'w')
    f_out_guid     = open(fn+'_guid'    + '.tsv', 'w')
    f_out_dtwrld   = open(fn+'_dtwrld'  + '.tsv', 'w')

    for line in f:
        elements = line[:-1].split('\t')
        parts_2 = elements[2].split('/')
        if len(parts_2) == 1:                 #the blank destination elements - '', plus the root domain ones
            if elements[1] == '/type/object/key':
                f_out_types.write( line )
            else:
                f_out_props.write( line )

        elif elements[2] == '/lang/en':
            f_out_props.write( line )

        elif (parts_2[1] == 'wikipedia' or parts_2[1] == 'authority') and len( parts_2 ) > 2:
            f_out_extkeys.write( line )

        elif parts_2[1] == 'm':
            f_out_m.write( line )

        elif parts_2[1] == 'en':
            f_out_intkeys.write( line )

        elif parts_2[1] == 'source' and len( parts_2 ) > 2:
            f_out_src.write( line )

        elif parts_2[1] == 'user':
            f_out_usr.write( line )

        elif parts_2[1] == 'base' and len( parts_2 ) > 2:
            if elements[1] == '/type/object/key':
                f_out_types.write( line )
            else:
                f_out_base.write( line )

        elif parts_2[1] == 'biology' and len( parts_2 ) > 2:
            f_out_blg.write( line )

        elif parts_2[1] == 'business' and len( parts_2 ) > 2:
            f_out_bus.write( line )

        elif parts_2[1] == 'soft' and len( parts_2 ) > 2:
            f_out_soft.write( line )

        elif parts_2[1] == 'uri':
            f_out_uri.write( line )

        elif parts_2[1] == 'quotationsbook' and len( parts_2 ) > 2:
            f_out_quot.write( line )

        elif parts_2[1] == 'freebase' and len( parts_2 ) > 2:
            f_out_frb.write( line )

        elif parts_2[1] == 'tag' and len( parts_2 ) > 2:
            f_out_tag.write( line )

        elif parts_2[1] == 'guid' and len( parts_2 ) > 2:
            f_out_guid.write( line )

        elif parts_2[1] == 'dataworld' and len( parts_2 ) > 2:
            f_out_dtwrld.write( line )

        else:
            f_out_types.write( line )

Save this as parse.py:

import sys

def parse_freebase_quadruple_tsv_file( file_name ):
    fn = file_name.split('.')[0]
    f = open( file_name )
    f_out_links = open(fn+'_links'+'.tsv', 'w')
    f_out_ns    = open(fn+'_ns'   +'.tsv', 'w')

    for line in f:
        elements = line[:-1].split('\t')

        if len( elements ) < 4:
            print 'Skip...'
            continue

        #print 'Processing ' + str( elements )                                                                                                                  

        #cases described here http://wiki.freebase.com/wiki/Data_dumps                                                                                          
        if elements[1].endswith('/notable_for'):                               #ignore notable_for, it has JSON in it                                           
            continue

        elif elements[2] and not elements[3]:                                  #case 1, linked                                                                  
            f_out_links.write( line )

        elif not (elements[2].startswith('/lang/') and elements[2] != '/lang/en'):   #ignore languages other than English                                       
            f_out_ns.write( line )

if len(sys.argv[1:]) == 0:
    print 'Pass a list of .tsv filenames'

for file_name in sys.argv[1:]:
    parse_freebase_quadruple_tsv_file( file_name )

Notes:

• Depending on the machine the index creation may take anywhere from a few to 12+ hours (consider the amount of data you are dealing with though).
• To be able to traverse the data in both directions you need an index on links.destination as well which I found to be expensive timewise and never finished.
• Many other optimizations are possible here. For example the 'types' table is small enough to be loaded in memory in a Python dict (see e.get_namespaced_data( 'freebase_ns_types.tsv' ))

And the standard disclaimer here. It has been a few months since I did this. I believe it is mostly correct but I do apologize if my notes missed something. Unfortunately the project I needed it for fell through the cracks but hope this helps someone else. If something isn't clear drop a comment here.