DATABASE npl_class: Parsing and Consolidation ?

[cverluise]

Hello,

Since v0.2-npl, we have introduced a DATABASE npl_class

Question

How should this class of citations be structured and consolidated?

Food for thoughts

Below is a sample of 100 citations for this class.

WITH
  tmp AS (
  SELECT
    npl_publn_id
  FROM
    `npl-parsing.patcit.v02_npl`
  WHERE
    npl_class="DATABASE")
SELECT
  npl_biblio
FROM
  `usptobias.patstat.tls214` AS tls214,
  tmp
WHERE
  tmp.npl_publn_id = tls214.npl_publn_id
LIMIT 100  

Row	npl_biblio
1	GENESEQ Database, Search Date Sep. 8, 2003 Accession No. P AAE04230 (Ruben SM et al.), Pub Date May 25, 2001.
2	Lerner et al., GenBank Accession No. AAB42052 (U39534.1), submitted Oct. 27, 1995.
3	Database Registry Accession No. RN 922391-60-4; Entered STN: Feb. 22, 2007.
4	Pritzlaff et al., 'Streptococcus agalactiae cyl gene cluster, partial sequence,' GenBank Accession No. AF157015, Feb. 8, 2001.
5	GenBank Accession No. U91324 for, Human chromosome 2 BAC clone CIT987SK 100B4 complete sequence Mar., 1997.
6	NCBI Sequence NM-003012, 'Homo sapiens secreted frizzled-related protein 1 (SFRP1), mRNA,' pp. 1-6, http://www.ncbi.nih.gov, printed May 5, 2006.
7	GenBank: AY383628.1. Synthetic construct HPV18 major capsid protein L1 (L1) gene, complete cds. Published on Oct. 11, 2003.
8	Chong, S.S., et al. (GI 450532), GenBank Sequence Database (Accession X71355), National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, 20894. No date provided.
9	NCBI annotation project, GenBank Accession Number, XP-002252, Oct. 2001.
10	DATABASE UNIPROTKB [online] 20 December 2005 (2005-12-20), retrieved from http:l/www.uniprot.org/uniprot/POAFQO Database accession no. POAFQO
11	UniProt Accession No. D1MAM0, Full=Tyrosine-protein kinase receptor; EC=2 . 7 . 10 . 1, 2010, XP-002656286, two pages.
12	Database accession No. RN 1144428-37-4; XP-002745331; (May 8, 2009) Supplier: Interbioscreen Ltd.; 1 page.
13	Database Swissprot-42 Accession No. Q57124, Nov. 10, 1997, 1 page.
14	Database STN Abstract: Accession No. 1984:603807 CAPLUS, Document No. 101-203807, 'Metabolism and disposition of 3-amino-1,5-dihydro-5-methyl-1-beta-D-ribofuranosyl-1,4,5,6,8-pentaazaacenaphthylene in the rat', Basseches et al., Cancer Research 1984, 44(9), 3672-8.
15	GenBank Accession No. CJ669561 'CJ669561 Y.Ogihara unpublished cDNA library Wh-KMV Triticum aestivum cDNA clone whkv19d01 5-, mRNA. sequence' dated Feb. 23, 2013.
16	Genebank Accession No. CY041637.
17	GENESEQ Database, Search Date Sep. 8, 2003 Accession No. P AAB31202 (Ashkenazi AJ et al.), Pub Date Dec. 21, 2000.
18	GenBank Accession No. XP-001273036.1, published Feb. 21, 2008.
19	Database Uniprot Database accession No. B9SXX3.
20	DATABASE PUBCHEM. [o] 13 February 2015 (2015-02-13), Database accession no. 15257684.
21	Geneseq [Online] Oct. 23, 1998, 'Streptococcus pneumoniae genome fragment SEQ ID No. 214.' retrieved from EBI accession No. GSN: AAV52347, Database accession No. AAV52347 (the whole document).
22	Database Registry [Online] Chemical Abstracts Service, Columbus, Ohio, US; Jun. 10, 2008, 'Not yet assigned', Database accession No. 1027012-36-7 the whole document.
23	DATABASE UniProt EMBL; 1 November 1997 (1997-11-01), retrieved from UNIPROT accession no. Q24733
24	NCBI Entrez, Genbank Report, Accession No. AA154256, Marra, M. et al. (Feb. 1997).
25	Marra et al., 1997, GenBank Accession No. AA170532.
26	GenBank Accession No. AA281296.
27	NCBI GenBank Accession No. EU216059, Homo sapiens BCR/ABL fusion protein isoform X2 (BCR/ABL fusion) mRNA, complete cds; http://www.ncbi.nlm.nih.gov/nuccore/EU216059.1?report=gbwithparts&log$=seqview, printed Aug. 8, 2012 2 pages.
28	Genbank Entry, Accession No. AA010038 (1996).
29	Geneseq Database Accession No. Y00771 (Jan. 21, 1999).
30	NCBI Reference sequence: XP-001164530, Sep. 15, 2006.
31	Genbank Accession No. AI492143 (Mar. 30, 1999).
32	Database EMBL, entry HSGS04157, Accession No. D25789, Nov. 27, 1995.
33	'GENBANK', Database accession no. AAF172491
34	GenBank Accession No. AB333793.1 (2008).
35	GenBank Accession No. AA178778 (1997).
36	Genbank Submission; NCBI, Accession No. NP-049542; Xiao et al.; Mar. 11, 2010.
37	GenPept, Accession No. CAA72296, Mouillet J.F., Tenebrio molitor mRNA for ecdysone receptor.
38	GenBank Accession No. U65416 (gi:1815636), 'Human MHC class I molecule (MICB) gene, complete cds,' Feb. 5, 1997.
39	NCBI Database Report for Accession No. BAD59440, Direct Submission on Sep. 26, 2003.
40	Wilson (2007, GenBank Accession No. AC 190815).
41	GenBank Accession No. Q9WWD3, created Nov. 1, 1999.
42	Fleischmann, R.D. et al., (GI 1574563), GenBank Sequence Database (Accession U32844; L42023), National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, 20894.
43	‘Duck Tales,’(1987)[TV Series 1987-1990], Internet Movie Database (IMDB) [Retrieved on Apr. 7, 2007].
44	Hillier et al., Genbank Accession No. AA149044 (May 19, 1997).
45	Marra et al., 1997, GenBank Accession No. AA423158.
46	NCBI NP-075598.2 Basic Fibroblast growth factor receptor 1 isoform 1 precursor [Homo sapiens] [online] Dec. 13, 2009. Available on the internet: http://www.ncbi.nlm.nih.gov/protein/NP-075598.2.
47	NCBI Locus Report for TP43 (www.ncbi.nlm.gov/gene?term=7157) Last visited Sep. 29, 2014.
48	GenBank Submission; NIH/NCBI, Accession No. NM-014707, Muralidhar et al.; Mar. 11, 2011.
49	GenBank Accession AC007869
50	Database EMBL Accession No. P02643 Jul. 21, 1986 XP-002275449.
51	'Topic Real-Time', HP-UX-Documentation Disc 50726-10186 (from Software Patent Institute Database of Software Technologies), Feb. 1, 1995.
52	GenBank accession number WP_003406912; 6/22/2013
53	GenBank Accession No. AEK08729 dated Feb. 23, 2005, 2 pages.
54	DATABASE REGISTRY, vol. RN 202207-27-0, JPN6018008407, 5 March 1998 (1998-03-05)
55	GenBank Accession No. AA532364 for nj12a08.s1 NCI-CGAP-Pr22 Homo sapiens cDNA clone IMAGE:986102 3', mRNA sequence.
56	EMBL Sequence Data Library Accession No: O48889, Jun. 01, 1998, Bolchi, A. et al.
57	Database Registry, XP-002336813, May 19, 1989, RN-120685-11-2, 2 pages.
58	Albrandt et al., 'Human Uncoupling Protein 4,' Database: A_Geneseq_36, Accession No. Y78511, 2000.
59	《GenBank》 20081204 Kikuchi,S.等 AK062614 序列表 1，2 , 2
60	Database Caplus on STN: Accession No. 1976-519336 (1976).
61	GenBank GI No. 116875767; Accession No. NP 003248.3, dated Oct. 31, 2006, 7 pages.
62	Yin, D.X. et al., (Direct Submission), GenBank Sequence Database (Accession U66879), National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, 20894 (GI 1683636; GI 1683637) Nov. 23, 1996.
63	Hillier, L. et al. Wash U-Merck EST Project Genbank Accession No. 1264408 May 26, 1995.
64	GENBANK Accession No. Z32768 1994 'Human coronavirus OC43 gene for surface protein', 3 pages.
65	Pring-Akerblon, Hexon Protein-Human Adenovirus 4, Accession No. S57637, submitted to the EMBL Data Library, (Feb. 1995).
66	Database accession No. 147:166330 abstract, Database CAPLUS, Chemical Abstracts Service, Columbus Ohio, US, Retrieved from STN accession No. 2007:711051, 2007, 1 page.
67	GenBank Accession No. AA746653 for Homo Sapiens cDNA clone 1257327; Jan. 22, 1990.
68	DATABASE EMBL DATABASE 'Extract V00320'
69	GenBank Accession No. AB020693 dated Jan. 10, 2004.
70	GenBank Submission; NIH/NCBI, Accession No. EAS23724; Mar. 22, 2006.
71	Ink A Dink A Do, 4 Inks in One, Stamp Pad (undated).
72	GenBank Accession No: AA242576, Mar. 7, 1997.
73	Haecker, Genbank Accession M96441 Medline 92409595, May 5, 1993.
74	Database Biosis, Biosciences Information Service, Philadelphis, PA, k. Fujita et al., 'Effects of flunarizine on primary open angle and low tension glaucomas'.
75	Genbank No. AAG10021 dated Sep. 3, 2000.
76	Sasaki T., EMBL Database, Aug. 6, 1997, Rice CDNA from callus, XP00212812.
77	Genbank Accession No. W97816 (Soares mouse embryo NbME13.5 14.5 cDNA) Jul. 16, 1996.
78	NCBI Entrez Accession No.: gil14149916, submitted May 2000.
79	Database GenBank (EST); Accession No: A1987883; Marra et al. mouse clone; Sep. 2, 1999; Having at least 18 and 50 contiguous nucleotides of SEQ ID NO: 5.
80	NCBI, (mRNA Sequence) Accession No. AI925946, 'wh12f04.x1 NCI-CGAP-Kid11 Homo sapiens cDNA clone Image: 2380543 3- similar to TR:O00581 O00581 Hypothetical 20.5 KD Protein.', [retrieved on Apr. 19, 2011] Retreived from the Internet <URL:http://www.ncbi.nlm.gov/nucest/5661910?report=genbank.
81	EMBL Database Report for Accession No. 24995, dated Nov. 9, 1992.
82	Database EBI Accession No. UniProt: A1JRX1, Feb. 6, 2007, Isocitrate lyase, XP-002576046.
83	GenBank Accession No. AK001872.1, 'Homo sapiens cDNA FLJ11010 fis, clone PLACE1003145', pp. 1-2, (submitted Feb. 16, 2000).
84	GenBank Accession No. AK055917, published Jan. 19, 2008.
85	GenBank accession 000375 Jun. 1997.
86	Net core GenBank accession No. AF069670.
87	NCBI (2005) Accession NP-566186.
88	GenBank Accession No. AE000554. Aug. 6, 1997.
89	Database Caplus (Online), Chemical Abstracts Service, XP000002657265, Database accession No. 2005:1235680 abstract & CN 1 596 742 A, (2005).
90	Rouse et al. GenBank Accession No. A54805, Oct. 28, 1994.
91	GenBank Accession No. AF490589, Arabidopsis thaliana Na+/H+ exchanger 5 (NHX5) mRNA, complete cds, 2002.
92	Vogel, P. et al., (GI 1834507), GenBank Sequence Database (Accession Z50781), National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, 20894.
93	GenBank Accession No. Q9Y5S2.
94	NCBI Accession No. P08176(DerP1) 9 pages.
95	Gray, et al., Maturase [Neosartorya fischeri] GenBank Accession No. AAX39426, May 19, 2005.
96	GENBANK nucleotide sequence AB008394 (Mar. 14, 1009).
97	EMBL Database, Accession No. U80669, Prescott, J.S. et al. 'Human androgen regulated homeobox protein (NKX3.1) mRNA, complete cds' (Dec. 1996).
98	DATABASE GENBANK 5 March 1996 (1996-03-05), CHEN XY. ET. AL.
99	Genbank Accession No. AI867518 (Dec. 17, 1999).
100	GenBank Accession No. CAB03914 for C24H11.8, Nov. 23, 1998.

Open questions

• Need for further sub-classification? If yes, which sub-classes?
• Fields to be parsed?
• Corpus/ reference database for consolidation?

I leave these questions open to discussion.

Cheers

[gderasse]

This is tricky. We could try searching for the database on https://datasetsearch.research.google.com/ but I am not convinced it is a fruitful direction.
1/ Many entries are related to GenBank, so we could probably seek to consolidate NPL for a few selected databases.
2/ Otherwise, we could ask the EPO for a list of the databases they have access to. After all, examiners must have access to these databases for performing examination.

[cverluise]

Some thoughts on the parsing approach:

• database_name (e.g. GENBANK, EMBL, NCBI, etc)
• accession_number (e.g. Y78511, 1976-519336, etc) -> key for consolidation
• accession_year (e.g. 2006)
• bibliographical_reference (e.g Prescott, J.S. et al. 'Human androgen regulated homeobox protein (NKX3.1) mRNA, complete cds' (Dec. 1996), row 97)
• locus (e.g. C24H11.8, NKX3.1) -> key for consolidation? enrichment?