Validation of scientific articles with zotero

In order to complete the previous post, I uploaded a couple of videos; they show out how to search and import in zotero a scientific article found in google scholar, and then how to export it in Bibtex (and then straight into Jabref).

I start from an access DB containing a batch of records I had to clean & validate so I decided to use google scholar as parse & validation tool. Then Zotero & Jabref did the rest.

IMPORTING IN ZOTERO FROM GOOGLE SCHOLAR




EXPORTING FROM ZOTERO TO BIBTEX

Creating a scientific literature database with zotero and jabref

If we need to create a database of our own, for scientific literature, without going through the expensive services of Thomson, Elsevier or other data provider, there are some wonderful (and free of cost) tools who may help.

Let's figure we need to create/validate a list of scientific articles references; an easy way could be to use google scholar, by looking for the articole/journal title.
Ok, then?
Then we may use zotero, a firefox extension that help in collecting and managing data of articles and supports export in formats like Bibtex, refer, RIS and many others.
In other words, zotero is nothing but an xtml parser, able to recognize from the webpage what kind of publication (book, article, webpage, proceeding) is facing, and download the relevant informations.

After zotero, in order to handle better and have even more export forrmats (like MySQL fi) I suggest to use jabref, another free tool, that can be feeded from Zotero by exporting data in Bibtex.

With the two of them we can build and handle any dimension of scientific literature DB

EPO patenting activity by NUTS3

Recently I had to create a benchmark for the patenting activity on EPO patents (based on patstat 10/2009) by weighting each patent by inventors' nuts3.

The result was someway amazing 'cause it seems that the TOP25 (I'm publishing below here) has many EU areas in a higher position than the first US area. The first EU area is from Holland, not from Germany as we could expect from te total count of patents...

NUTS3	CY	COUNT	LOCATION
JPC13	JP	102503,082	TOKYO
JPF27	JP	32278,605	OSAKA
NL414	NL	22388,468	EINDHOVEN
JPE23	JP	22307,48	AICHI
FR101	FR	21689,393	PARIS
DE212	DE	16782,779	MUNCHEN
JPC11	JP	16390,328	SAITAMA
JPF28	JP	14888,869	KOBE
FR105	FR	14340,232	BOULOGNE BILLANCOURT
ITC45	IT	14030,154	MILANO
JPC08	JP	13297,203	YOKOHAMA
JPC12	JP	11934,707	CHIBA
25017	US	11879,31	FRAMINGHAM/ACTON
SE010	SE	11489,587	STOCKHOLM
KR013	KR	11158,808	SUWON-SI
JPC22	JP	11031,511	SHIZUOKA
CH040	CH	10752,436	ZURICH
36055	US	10563,428	ROCHESTER
DE300	DE	10329,677	BERLIN
06037	US	10057,301	REDONDO
JPF26	JP	9562,31	KYOTO
06085	US	9378,459	MOUNTAIN VIEW
JPD17	JP	9260,929	YOKOHAMA-SHI
DE115	DE	8883,498	LUDWIGSBURG
FR714	FR	8711,347	GRENOBLE
FR103	FR	8603,364	VERSAILLES

a VBA function counting chars

It may happen to find in some data sources more than one occurence of a data type inside the same field, separated by a special char.
But in many cases that  char may be not so special and be misguiding when trasposing the field.
Let's take as example Thomson SDC database, where in the alliance name you find the alliance participants names separated by the / char.
Obviously the / char may also be integral part of some participant name; so we need to count the occurrence of the / char in order to compare it to the number of partipants indicated in the same record in order to do futher cleaning, if needed.

So I wrote a small DBA function called CHARCOUNT, and I'm posting it here

Function charcount(inputstring As String, findstring As String)
' return the number of occurrences of findstring in inputstring

Dim a$, b$
Dim c, i As Integer

a$ = inputstring
b$ = findstring

c = 0
For i = 1 To Len(a$) - Len(b$) + 1
    If Mid(a$, i, Len(b$)) = b$ Then
        c = c + 1
    End If
Next

charcount = c

End Function
Function charcount(inputstring As String, findstring As String)
' return the number of occurrences of findstring in inputstring

Dim a$, b$
Dim c, i As Integer

a$ = inputstring
b$ = findstring

c = 0
For i = 1 To Len(a$) - Len(b$) + 1
    If Mid(a$, i, Len(b$)) = b$ Then
        c = c + 1
    End If
Next

charcount = c

End Function

Introducing chinese patents into PATSTAT

PATSTAT documentation says the raw data cover more than 90 patent office.
The question is how, and at what extent. In this post I start an investigation about SIPO patents that will last for some weeks.

The EPO’s co-operation with the State Intellectual Property Office of the People’s Republic of China (SIPO) is based on an agreement signed on 11 June 1985. An EPO-SIPO Joint Committee meets once a year to review relations and approve the following year’s program of activities. The co-operation was significantly enhanced in 1997 when EPOQUE ( an international search database for patents)  was made available to SIPO.
The overall objective is to facilitate trade between China and Europe by supporting China’s efforts to develop a modern and effective system for IPR protection. EPO aims to improve the quality of SIPO work as the Chinese patent system expands. 

To ensure equal quality standards of granted patents , the majority of the SIPO's 2,000+ patent examiners have been trained by the EPO. An additional 60 examiners per year receive training at EPO centres in The Hague, Munich and Vienna.

Since mid-1990s, the SIPO adopted the EPOQUE system,and as a result compatibility of archived patent information is now the basis of all digital data exchange.

EPO and the SIPO share patent databases with synchronization at weekly intervals. The SIPO has also recently opened its 32 000-entry database on traditional Chinese medicine to the EPO and its member states.

Here is a selection of the most relevant INPADOC-Newsletters referring to Chinese patent data, kind codes and number formats used in the INPADOC database (the links below are pointing to PDF files):

Newsflash 2005/16: Completion of Load of Backlogged Chinese Data (PDF)
Inpadoc Patent Gazette Newsletter 01/05 (PDF)
Inpadoc Patent Gazette Newsletter 02/04 (PDF)
Newsflash 2005/05: New CN Application number format and updates of Chinese bibliographic data (PDF)
Newsflash 2005/02: Change in kind codes of Chinese documents (PDF)
IPG-Newsletter 99/10: Translation of PCT application into Chinese language (PDF)
Newsflash 2005/25: Chinese application numbers (continued) (PDF)
Newsflash 2006/14: Reload of Chinese A, C and Y documents intended for the inclusion of Chinese language elements (PDF)
Newsflash 2004/17: Legal Status Data from Hong Kong (PDF)
Patent Information Supplement 09/2009
Newsflash 11/2009: Chinese legal status data in the EPO INPADOC database
Newsflash 11a/2009: Chinese legal status data in the EPO INPADOC database (update)
IPG-Newsletter 3/2005

Also EPO FAQ about china patents may be useful

  In mid-2009, the EPO has started uploading English legal status data for both Chinese patents and utility models documents as part of the INPADOC legal status information in esp@cenet.
The data upload commenced in week 18/2009;  the collection should include over 6.7 million records and cover all Chinese legal status events for patent and utility model applications in China dating back to October 1985.
 
You can obtain legal status information in English via the Chinese Patent Office's (SIPO) databases on the China Intellectual Property Net . All the above-mentioned sources there is a time delay of several months for legal status information in English.

data from SIPO: Annual Applications for Patents 

Year	Total
1999	134239
2000	170682
2001	203573
2002	252631
2003	308487
2004	353807
2005	476264
2006	573178

in forthcoming posts we're going to analise the coverage in PATSTAT against such figures

References

EPO international relation： http://www.epo.org/about-us/office/international-relations/projects/china.html
EPO and SIPO move ahead to secure IPR: http://www.epo.org/topics/news/2008/20080606.html

European patents and patent applications - statistics 2008: http://www.epo.org/about-us/office/statistics.html
Patent Information News 2/2009: http://www.epo.org/about-us/publications/patent-information/news/2009.html

Thanks for help in collecting the information to Kun Fu 

Origin of citations in European Patent Office

Whenever you'd need to understand who introduces a citation to a patent in PATSTAT, you may look at  table TLS212_citation, where you may find the field CITN_ORIGIN.

The content of such field may be any of these


0 - SEA- citations introduced during search
1 - APP- citations introduced by the applicant
2 - EXA- citations introduced during examination
3 - OPP - citations introduced during opposition
4 - 115- citations introduced according to Art 115 EPC
5,6 not public



Let's see the content of this field in EPO patents (count made on PATSTAT 10/2009 grouping by publication numbers)

ORIGIN        COUNT OF CITATIONS

0                    22985072

1                     6175203

2                      178744

3                       15839

4                       13533

While in in USPTO patents..
(count made with same criteria as above)

ORIGIN        COUNT OF CITATIONS
0              37425072 
1              15534910

The higher number of applicant introduced citations is due to the "duty of candor" rule which imposes the disclosure of all prior art.

Patstat and patent families

As wikipedia says, a patent family is "a set of patents taken in various countries to protect a single invention". Another way to say it is to call the patents belonging to the same family as 'equivalents'.

Infact when using ESPACENET and searching FI patent EP100000 you will see on rightmost side of your browser a list of "also published as" (1) that can be listed more in detail by going on "View INPADOC patent family" (2).


But we must be careful cause with patents, as in real  life, is very hard to give a unique definiton of what a family is...

In patstat from april 2009 two new tables have been introduced in order to help users to build a table of equivalents: tls218_DOCDB_FAM and tls219_INPADOC_FAM.

the first, tls218_DOCDB_FAM (SIMPLE FAMILY) gives the same family id to applications claiming exactly the same prior applications as priorities (these can be Paris Convention priorities or just technical relation priorities).
As PATSTAT documentation says: "The EPO reserve the right to classify an application into a particular simple family irrespective of this general rule" This is done by creating artificial priorities for an application to force it to match the priorities of a family.
The simple family is also at times used to attribute automatically the same IPC classification symbols and other attributes to corresponding applications.

The latter, tls219_INPADOC_FAM, (extended priority family) was developed by the INPADOC organisation then integrated by EPO.
In this case the linkage among applications can come from connections in tables TLS204_appln_prior (PARIS convention priorities) , TLS205_TECH_REL (patents which have been technically linked by patent examiners on the basis of similar content) and table TLS216_appln_contn (continuations, divisions etc).
The artificial PATSTAT applications due to priorities which have no entry in DOCDB are also included in this family.
The artificial PATSTAT applications due to unknown cited publications are included in this family table , but they all appear as a family with 1 member only.

Maybe an example can make things clearer: if we consider the group of applications D1..D5

Document D1    Priority P1

Document D2    Priority P1    Priority P2

Document D3    Priority P1    Priority P2

Document D4                   Priority P2    Priority P3

Document D5                                  Priority P3

While for INPADOC all documents will belong to one family only, for EPODOC we will have

FAMILY1: D1
FAMILY2: D2, D3
FAMILY3: D4
FAMILY4: D5

Or if you want a real case, I selected to which DOCDB and INPADOC family was belonging the application with patstat appln_id = 1; the difference is very evident.


DOCDB family           

APPLN_ID     DOCDB_FAMILY_ID    appl_auth    APPLN_NR

1            25590760            'AL'     '        9600001'

889876       25590760            'AT'     '       96931674'

1806521      25590760            'AU'     '        7081996'

18755226     25590760            'ES'     '       96931674'

               
INPADOC               

APPLN_ID     INPADOC_FAMILY_ID    appl_auth    APPLN_NR

1            3960163              'AL'     '        9600001'

889876       3960163              'AT'     '       96931674'

1806521      3960163              'AU'     '        7081996'

14573559     3960163              'DE'     '       69602451'

14573560     3960163              'DE'     '       69602451'

17633931     3960163              'EP'     '       96931674'

18755226     3960163              'ES'     '       96931674'

24291685     3960163              'GR'     '       99401928'

47191406     3960163              'US'     '        2963998'

57000038     3960163              'AL'     '           4195'

59131347     3960163              'EP'     '        9503551'

Limits of DOCDB and INPADOC

We may say the DOCDB families are sometimes too restrictive, since they do not put divisionals, continuations etc. into the same family although they should. Also the same appln_id may occur in more than one DOCDB family.

The INPADOC on the other side shows highly related patent documents, even if they are not necessarily on the same aspect of the invention. The same application id only occurs in one family, but the family is typically very comprehensive.

Other definitions:

Dietmar Harhoff at LMU developed a definition of equivalents allocating patents into one group/family of equivalents if they have the same priorities, and then it aggregates those groups across which members occur more than once.

Also Derwent developed a definition of patent family and here you can find some details.

(Thanks to Fabio Montobbio and Raffaele Conti for helping me in information collection for this post)