Patent Data Processing - SQL Steps

Project

Patent Data Processing - SQL Steps
Project Information
Has title	Patent Data Processing - SQL Steps
Has owner	Shelby Bice
Has start date
Has deadline date
Has keywords	Tool
Has project status	Subsume
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Return to Patent Data (Wiki Page).

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.

Index

Since the table is relatively large, and is likely to be searched often, an index has been imposed on the table.

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

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

Patentdata Schema:

Column  |       Type        | Modifiers
--------+-------------------+-----------
patent  | integer           |
kind    | character varying |
claims  | integer           |
apptype | integer           |
appnum  | integer           |
gdate   | date              |
gyear   | integer           |
appdate | date              |
appyear | integer           |

Patent_2015 Schema:

            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    |
 

Overlapping Columns

  patent_data     patent_2015
 --------------+-------------
   patent      |  patentnumber
   kind        |  kind
   claims      |  numberofclaims
   apptype     |  type
   appnum      |  applicationnumber
   gdate       |  grantdate
   appdate     |  filingdate
   

Combined Schema:

The final schema of the patents table is :

          Column        |       Type        | Modifiers
  ----------------------+-------------------+-----------
   patent               | integer           | not null
   grantdate            | date              |
   prioritydate         | date              |
   prioritycountry      | character varying |
   prioritypatentnumber | character varying |
   cpcsubgroup          | character varying |
   pctpatentnumber      | character varying |
   claims               | integer           |
   appnum               | integer           |
   gyear                | integer           |
   appdate              | date              |
   appyear              | integer           |
   nber                 | integer           |
   uspc                 | character varying |
   uspc_sub             | character varying |

From the total list of columns belonging to both the tables (patentdata and patent_2015), a few columns, most of them related to classification of patents, have been dropped since the data in the tables was not clean.

Additionally, three columns - nber, uspc, uspc_sub have been added from the historicalpatentdata, a table built from data downloaded from the USPTO Bulk Data Storage. The join was executed on the patent number.

 Note : The addition, deletion of columns as through separate scripts, therefore the scripts below will be slightly discrepant.
       

Index and Key Creation

Patent numbers are distinct in this table, and are central to the rest of the fields in the table. A primary key can therefore be imposed on the column. Also, since a number of searches are likely to be conducted on this table, an index has been imposed as well.

Code:

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

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)

Citations

In the citations table, we needed to define another function that would convert a textual patent number into a number (big int, since the patents number were exceeding the range of regular integers.)

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 schema:

   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 schema:

        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

Overlapping Columns

      patent_2015     |  patentdata   |
 ---------------------+---------------+
  citingpatentnumber  | patent        |
  citedpatentnumber   | citation      |
 

Combined Schema:

      Column       |  Type  | Modifiers

---

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

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

The USPTO has a repository of patent data on their Bulk Data Storage system. We have this data downloaded and loaded into a table on the patent database. Here are the steps followed:

• Download file from the BDS system - we have access to CSV files.
• Create table with required specs
• use the \COPY command to copy the data from the file into the table.

Script follows.

Script:

/* 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