Patent Data Processing - SQL Steps

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Objective

The McNair Center owns two sets of patent data - one set that is inherited from Harvard, the Harvard dataverse, which is stored in the database patentdata and another that is generated by crawlers pulling data from the USPTO website, which is stored in the database patent_2015.

We are now merging and cleaning the two data sets, and storing them in a schema that is amalgamation of the two underlying schema for the citations tables, assignees tables, and patents tables. The destination schema is allpatent.

Assignees Data

The schema for the assignees table in patentdata database is: 

  Column    |       Type        | Modifiers

+-------------------+----------- 

patent      | integer           |
asgtype     | integer           |
assignee    | character varying |
city        | character varying |
state       | character varying |
country     | character varying |
nationality | character varying |
residence   | character varying |
asgseq      | integer           |

The schema for the assignees table in patent_2015 is : 

   Column     |  Type   | Modifiers

+---------+----------- 

lastname      | text    |
firstname     | text    |
orgname       | text    |
city          | text    |
country       | text    |
patentcountry | text    |
patentnumber  | integer |
state         | text    |
address       | text    |
postcode      | text    |

To merge both schemas, we have some columns that overlap, and some columns that don't.

Overlapping Columns 

patent_2015  | patentdata

+-------------- 

orgname      | assignee 
city         | city 
country      | country
patentnumber | patent 
state        | state

These columns will have entries for most rows in the table, because they exist in both tables. The rest of the columns will be populated based on which table the row is coming from.

Final Schema 

        Table "public.assignees"
   Column     |       Type        | Modifiers

+-------------------+----------- 

lastname      | character varying |
firstname     | character varying |
address       | character varying |
postcode      | character varying |
orgname       | character varying |
city          | character varying |
country       | character varying |
patentnumber  | integer           |
state         | character varying |
patentcountry | character varying |
nationality2  | character varying |
residence     | character varying |
asgseq        | integer           |
asgtype       | integer           |

Non-overlapping Columns These are the columns that belong to either one of the assignees tables, and not to both. For these cases, to help users understand where the row is coming from, the following insert rules have been followed:

  • For columns of type int, insert -1
  • For columns of type string (character varying), the string 'null' has been inserted.

Therefore, if a row has appropriate values for orgname, state, city ,etc, but 'null' values for lastname, firstname, address and postcode, the row has come from the patentdata table.

Sample insert and copy commands

INSERT INTO assignees_merge ( SELECT 'null', 'null', 'null', 'null', a.assignee, a.city, a.country, a.patent, a.state, 'null', a.nationality, a.residence, a.asgseq, a.asgtype FROM assignees a );

INSERT INTO assignees_merge ( SELECT assignees.lastname, assignees.firstname, assignees.address, assignees.postcode, assignees.orgname, assignees.city, assignees.country, assignees.patentnumber, assignees.state, assignees.patentcountry, 'null', 'null', -1, -1 FROM assignees );


\COPY assignees_merge TO '/tmp/assignees_merge_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; \COPY assignees FROM '/tmp/assignees_merge_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --1607724

\COPY assignees_merge TO '/tmp/assignees_merge_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; \COPY assignees FROM '/tmp/assignees_merge_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --3818842

Note : The assignees table was updated on 6/23 to remove the 'null' string and the '-1' values.

Patents

INDEX CREATION

ALTER TABLE patents ADD PRIMARY KEY (patentnumber); -- RESULT : ALTER TABLE allpatent=# CREATE UNIQUE INDEX patent_idx ON patents (patentnumber);

allpatent=# CREATE INDEX ON assignees (orgname); CREATE INDEX

Patentdata: Column | Type | Modifiers

+-------------------+----------- 

patent  | integer           |
kind    | character varying |
claims  | integer           |
apptype | integer           |
appnum  | integer           |
gdate   | date              |
gyear   | integer           |
appdate | date              |
appyear | integer           |

Patent_2015:
            Column             |  Type   | Modifiers
-------------------------------+---------+-----------
 patentnumber                  | int | not null
 kind                          | varchar    |
 grantdate                     | date    |
 type                          | varchar    |
 applicationnumber             | varchar    |
 filingdate                    | date    |
 prioritydate                  | date    |
 prioritycountry               | varchar    |
 prioritypatentnumber          | varchar    |
 ussubclass                    | varchar    |
 maingroup                     | varchar    |
 subgroup                      | varchar    |
 cpcsubclass                   | varchar    |
 cpcmaingroup                  | varchar    |
 cpcsubgroup                   | varchar    |
 classificationnationalcountry | varchar    |
 classificationnationalclass   | varchar    |
 title                         | varchar    |
 numberofclaims                | int |
 primaryexaminerfirstname      | varchar    |
 primaryexaminerlastname       | varchar    |
 primaryexaminerdepartment     | varchar    |
 pctpatentnumber               | varchar    |
 filename                      | varchar    |

Combined Schema:

Column Names: 

patent int,
kind varchar,
claims int,
apptype int,
appnum int,
gdate date,
gyear int,
appdate date,
appyear int



   patentnumber int, -- patent 
   kind varchar, -- kind
   grantdate date, --gdate
   type varchar,
   applicationnumber varchar,
   filingdate date,
   prioritydate date,
   prioritycountry varchar,
   prioritypatentnumber varchar,
   ussubclass varchar,
   maingroup varchar,
   subgroup varchar,
   cpcsubclass varchar,
   cpcmaingroup varchar,
   cpcsubgroup varchar,
   classificationnationalcountry varchar,
   classificationnationalclass varchar,
   title varchar,
   numberofclaims int,
   primaryexaminerfirstname varchar,
   primaryexaminerlastname varchar,
   primaryexaminerdepartment varchar,
   pctpatentnumber varchar,
   filename varchar
   claims int,
   apptype int,
   appnum int,
   gyear int,
   appdate date,
   appyear int
   
   
   Output Schema: patents
   
     CREATE TABLE patents_merged( 
       patentnumber int, 
       kind varchar, 
       grantdate date,
       type varchar,
       applicationnumber varchar,
       filingdate date,
       prioritydate date,
       prioritycountry varchar,
       prioritypatentnumber varchar,
       ussubclass varchar,
       maingroup varchar,
       subgroup varchar,
       cpcsubclass varchar,
       cpcmaingroup varchar,
       cpcsubgroup varchar,
       classificationnationalcountry varchar,
       classificationnationalclass varchar,
       title varchar,
       numberofclaims int,
       primaryexaminerfirstname varchar,
       primaryexaminerlastname varchar,
       primaryexaminerdepartment varchar,
       pctpatentnumber varchar,
       filename varchar,
       claims int,
       apptype int,
       appnum int,
       gyear int,
       appdate date,
       appyear int
       );

Sample Insert and Copy Statements 

   patentdata:
   INSERT INTO patents_merged
   (
   		SELECT	
   		patent,

kind, gdate, 'NULL', 'NULL', NULL, NULL, 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', -1, 'NULL', 'NULL', 'NULL', 'NULL', 'NULL', claims, apptype, appnum, gyear, appdate, 

       	appyear
       	FROM patents
   );
   -- RESULT : INSERT 0 3984771
   
   patent_2015:
   INSERT INTO patents_merged
   (
   	SELECT
   		patentnumber,

kind, grantdate, type, applicationnumber, filingdate, prioritydate, prioritycountry, prioritypatentnumber, ussubclass, maingroup, subgroup, cpcsubclass, cpcmaingroup, cpcsubgroup, classificationnationalcountry, classificationnationalclass, title, numberofclaims, primaryexaminerfirstname, primaryexaminerlastname, primaryexaminerdepartment, pctpatentnumber, filename, -1, -1, -1, -1, NULL, 

       	-1
   	FROM patents
   );
   -- RESULT : INSERT 0 1646225

COPY SCRIPTS: patentdata: \COPY patents_merged TO '/tmp/merged_patents_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --COPY 3984771

patent_2015: \COPY patents_merged TO '/tmp/merged_patents_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --COPY 1646225

PATENTS TABLE \COPY patents FROM '/tmp/merged_patents_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; -- RESULT : COPY 3984771 \COPY patents FROM '/tmp/merged_patents_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; -- RESULT : COPY 1646225


TESTING

select count(*) FROM (SELECT DISTINCT patentnumber FROM patents) AS t; --RESULT: 5411151 EXPECTED: 5426566

We found some copies of a few rows, where both the patent_2015 and patentdata

SELECT COUNT(*), * FROM patents GROUP BY patentnumber, kind, grantdate, type, applicationnumber, filingdate, prioritydate, prioritycountry, prioritypatentnumber, ussubclass, maingroup, subgroup, cpcsubclass, cpcmaingroup, cpcsubgroup, classificationnationalcountry, classificationnationalclass, title, numberofclaims, primaryexaminerfirstname, primaryexaminerlastname, primaryexaminerdepartment, pctpatentnumber, filename, claims, apptype, appnum, gyear, appdate, appyear HAVING COUNT(*) > 1;

SELECT patentnumber, count(*) FROM patents GROUP BY patentnumber HAVING count(*)>1; --7640598


SELECT * FROM patents op WHERE op.patentnumber IN ( SELECT ip.patentnumber FROM patents ip GROUP BY ip.patentnumber HAVING COUNT(*)>1 ) ORDER BY op.patentnumber;

( SELECT * INTO patentsCleaned FROM patents op WHERE op.patentnumber IN ( SELECT ip.patentnumber FROM patents ip GROUP BY ip.patentnumber HAVING COUNT(*)=1 ) ORDER BY op.patentnumber ) --SELECT 5191306


INSERT INTO patentsCleaned( SELECT * FROM patents op WHERE op.patentnumber IN ( SELECT ip.patentnumber FROM patents ip GROUP BY ip.patentnumber HAVING COUNT(*)>1 ) AND op.applicationnumber NOT LIKE 'NULL' ORDER BY op.patentnumber );

--219845

TESTING: allpatent=# select count(*) from patentsCleaned; 

 count

5411151

(1 row)

allpatent=# select count(*), patentnumber FROM patentsCleaned group by patentnumber having count(*) > 1; 

count | patentnumber

+--------------

(0 rows)


                    • INDEX CREATION **************

ALTER TABLE patents ADD PRIMARY KEY (patentnumber); -- RESULT : ALTER TABLE allpatent=# CREATE UNIQUE INDEX patent_idx ON patents (patentnumber);

allpatent=# CREATE INDEX ON assignees (orgname); CREATE INDEX

Citations

To Extract Patents with Numbers Only and to Ignore Other RegExes CREATE OR REPLACE FUNCTION cleanpatno (text) RETURNS bigint AS $$ if ($_[0]) { my $var=$_[0]; if ($var=~/^\d*$/) {return $var;} return undef; } return undef; $$ LANGUAGE plperl;

patentdata: 

Column    |       Type        | Modifiers

+-------------------+----------- 

patent      | integer           |
cit_date    | date              |
cit_name    | character varying |
cit_kind    | character varying |
cit_country | character varying |
citation    | integer           |
category    | character varying |
citseq      | integer           |

SELECT patent as citingpatentnumber, citation AS citedpatentnumber INTO citations_merged FROM citations; --SELECT 38452957

patent_2015: 

Column        |  Type   | Modifiers

+---------+----------- 

citingpatentnumber  | integer |
citingpatentcountry | text    |
citedpatentnumber   | text    |
citedpatentcountry  | text    |

SELECT CAST(citingpatentnumber AS bigint), CAST(cleanpatno( citedpatentnumber) AS bigint) as citedpatentnumber INTO citations_merged FROM citations; -- RESULT : SELECT 59227881

FINAL TABLE:

CREATE TABLE citations ( citingpatentnumber bigint, citedpatentnumber bigint );


Copy Statements:

patentdata: \COPY citations_merged TO '/tmp/merged_citations_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --COPY 38452957

patent_2015: \COPY citations_merged TO '/tmp/merged_citations_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; -- RESULT : COPY 59227881

allpatent: \COPY citations FROM '/tmp/merged_citations_export.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --RESULT : COPY 59227881

\COPY citations FROM '/tmp/merged_citations_export1.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; --RESULT: COPY 38452957


CLONING: CREATE DATABASE allpatentsProcessed WITH TEMPLATE allpatent OWNER researcher;

USPTO Consolidated Patent Data

Scripts:

/* creating patent data tables from : https://bulkdata.uspto.gov/data2/patent/maintenancefee/*/

CREATE TABLE PatentMaintenanceFee( patentnumber varchar, applicationnumber int, smallentity varchar, filingdate date, grantissuedate date, maintenancefeedate date, maintenancefeecode varchar );

\COPY PatentMaintenanceFee FROM '/bulk/USPTO_Consolidated/MaintFeeEvents_20160613.txt' DELIMITER AS E'\t' HEADER NULL AS CSV; -- RESULT : COPY 14042059

/* creating tables for historical patent data - USPTO */

CREATE TABLE HistoricalPatentData( applicationid int, pubno varchar, patentnumber varchar, NBER int, USPC varchar, USPC_sub varchar, applicationdate date, prioritydate date, pubdate date, displaydate date, disptype varchar, exp_dt date, exp_dt_max date, pta int );

\COPY historicalpatentdata FROM '/bulk/USPTO_Consolidated/HistoricalFiles/historical_masterfile.csv' DELIMITER AS ',' HEADER NULL AS CSV;

--COPY 11191813

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