- Apr 2022
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metalpdb.cerm.unifi.it metalpdb.cerm.unifi.it
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narid:https://www.oxfordjournals.org/nar/database/summary/70
narCategory:Protein sequence databases
Subcategory:Protein sequence motifs and active sites
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motif.stanford.edu motif.stanford.edu
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narid:https://www.oxfordjournals.org/nar/database/summary/666
narCategory:Protein sequence databases
Subcategory:Protein sequence motifs and active sites
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- Mar 2022
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www.ebi.ac.uk www.ebi.ac.uk
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narid:https://www.oxfordjournals.org/nar/database/summary/646
narCategory:Structure Databases
Subcategory:Small molecules
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www.arb-silva.de www.arb-silva.deSilva1
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narid:https://www.oxfordjournals.org/nar/database/summary/1183
narCategory:Genomics Databases (non-vertebrate)
Subcategory:Taxonomy and identification
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yetfasco.ccbr.utoronto.ca yetfasco.ccbr.utoronto.ca
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narid:https://www.oxfordjournals.org/nar/database/summary/1462
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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pallab.serc.iisc.ernet.in pallab.serc.iisc.ernet.in
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narid:https://www.oxfordjournals.org/nar/database/summary/1339
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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ttsmi.bii.a-star.edu.sg ttsmi.bii.a-star.edu.sg
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narid:https://www.oxfordjournals.org/nar/database/summary/1765
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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github.com github.com
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http://www.tractor.lncc.br/
narid:https://www.oxfordjournals.org/nar/database/summary/756
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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https://insulatordb.uthsc.edu/
https://github.com/lmichan/BioDBS
narid:https://www.oxfordjournals.org/nar/database/summary/1063
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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tiprod.bioinf.med.uni-goettingen.de tiprod.bioinf.med.uni-goettingen.deHome1
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narid:https://www.oxfordjournals.org/nar/database/summary/904
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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www.nursa.org www.nursa.org
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narid:https://www.oxfordjournals.org/nar/database/summary/789
narCategory:Protein sequence databases
Subcategory:Protein localization and targeting
Category:Protein sequence databases
Subcategory:Databases of individual protein families
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rostlab.org rostlab.orgNLSdb1
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www.cbrc.kaust.edu.sa www.cbrc.kaust.edu.sa
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narid:https://www.oxfordjournals.org/nar/database/summary/1334
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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swissregulon.unibas.ch swissregulon.unibas.ch
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narid:https://www.oxfordjournals.org/nar/database/summary/1015
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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caps.ncbs.res.in caps.ncbs.res.in
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narid:https://www.oxfordjournals.org/nar/database/summary/1582
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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wwwmgs.bionet.nsc.ru wwwmgs.bionet.nsc.ruSELEX_DB1
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narid:https://www.oxfordjournals.org/nar/database/summary/246
narCategory:Nucleotide Sequence Databases, RNA sequence databases
Subcategory:TTranscriptional regulator sites and transcription factors, RNA sequence databases
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rulai.cshl.edu rulai.cshl.eduSCPD1
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narid:https://www.oxfordjournals.org/nar/database/summary/577
narCategory:Genomics Databases (non-vertebrate), Nucleotide Sequence Databases
Subcategory:Fungal genome databases, Transcriptional regulator sites and transcription factors
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stormo.wustl.edu stormo.wustl.eduScerTF1
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narid:https://www.oxfordjournals.org/nar/database/summary/1461
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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redfly.ccr.buffalo.edu redfly.ccr.buffalo.edu
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narid:https://www.oxfordjournals.org/nar/database/summary/1128
narCategory:Genomics Databases (non-vertebrate), Nucleotide Sequence Databases
Subcategory:Invertebrate genome databases, Transcriptional regulator sites and transcription factors
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linux1.softberry.com linux1.softberry.com
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narid:https://www.oxfordjournals.org/nar/database/summary/563
narCategory:Nucleotide Sequence Databases, Plant databases Subcategory:TTranscriptional regulator sites and transcription factors, General plant databases
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www.oreganno.org www.oreganno.org
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narid:https://www.oxfordjournals.org/nar/database/summary/1107
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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www.ifti.org www.ifti.orgooTFD1
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narid:https://www.oxfordjournals.org/nar/database/summary/185
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors wd:https://www.wikidata.org/wiki/Q111431789
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bhapp.c2b2.columbia.edu bhapp.c2b2.columbia.edu
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narid:https://www.oxfordjournals.org/nar/database/summary/1678
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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operondb.jp operondb.jp
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narid:https://www.oxfordjournals.org/nar/database/summary/846
narCategory:Genomics Databases (non-vertebrate), Nucleotide Sequence Databases
Subcategory:Prokaryotic genome databases, Transcriptional regulator sites and transcription factors
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gtrd.biouml.org gtrd.biouml.orggtrd1
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narid:https://www.oxfordjournals.org/nar/database/summary/1917
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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ccg.epfl.ch ccg.epfl.ch
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narid:https://www.oxfordjournals.org/nar/database/summary/823
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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narid:https://www.oxfordjournals.org/nar/database/summary/1082
narCategory:Nucleotide Sequence Databases, Structure Databases
Subcategory:Transcriptional regulator sites and transcription factors, Nucleic acid structure
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www.wikidata.org www.wikidata.org
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dbtss.hgc.jp dbtss.hgc.jp
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narid:https://www.oxfordjournals.org/nar/database/summary/591
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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asntech.org asntech.org
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narid:https://www.oxfordjournals.org/nar/database/summary/1837
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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coxpresdb.jp coxpresdb.jp
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narid:https://www.oxfordjournals.org/nar/database/summary/1062
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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bioinformatics.cs.vt.edu bioinformatics.cs.vt.edu
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narid:https://www.oxfordjournals.org/nar/database/summary/1058
narCategory:Genomics Databases (non-vertebrate), Nucleotide Sequence Databases
Subcategory:Prokaryotic genome databases, Transcriptional regulator sites and transcription factors
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rna.sysu.edu.cn rna.sysu.edu.cn
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narid:https://www.oxfordjournals.org/nar/database/summary/1594
narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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wwwmgs.bionet.nsc.ru wwwmgs.bionet.nsc.ruASPD1
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narid:https://www.oxfordjournals.org/nar/database/summary/308 narCategory:Nucleotide Sequence Databases
Subcategory:Transcriptional regulator sites and transcription factors
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research.bioinformatics.udel.edu research.bioinformatics.udel.edu
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narid:https://www.oxfordjournals.org/nar/database/summary/914
narCategory:Protein sequence databases
Subcategory:Protein properties
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memmorf.hegelab.org memmorf.hegelab.org
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hollywood.mit.edu hollywood.mit.edu
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hertellab.mmg.uci.edu hertellab.mmg.uci.eduHEXEvent1
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tomato.biodesign.asu.edu tomato.biodesign.asu.edu
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smartdb.bioinf.med.uni-goettingen.de smartdb.bioinf.med.uni-goettingen.de
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pombe.oridb.org pombe.oridb.orgOriDB1
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srs6.bionet.nsc.ru srs6.bionet.nsc.ruSRS61
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bioinfo2.ugr.es bioinfo2.ugr.es
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www-is.biotoul.fr www-is.biotoul.frISfinder1
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www.rna.whu.edu.cn www.rna.whu.edu.cn
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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rohsdb.cmb.usc.edu rohsdb.cmb.usc.edu
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github.com github.com
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www.clo-ontology.org www.clo-ontology.orgCLO1
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github.com github.com
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github.com github.com
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github.com github.com
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www.sbgnbricks.org www.sbgnbricks.org
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co.mbine.org co.mbine.org
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www.compgen.uni-muenster.de www.compgen.uni-muenster.de
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narid:https://www.oxfordjournals.org/nar/database/summary/1674
narCategory:Nucleotide Sequence Databases
Subcategory:Gene structure, introns and exons, splice sites
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wikidata-todo.toolforge.org wikidata-todo.toolforge.org
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www.wikidata.org www.wikidata.org
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- Feb 2022
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- EXAMPLE
- query SPARQL
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- Nov 2021
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www.wikidata.org www.wikidata.org
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Zotero can also export in (English) Wikipedia citation template format.
Using: Open Zotero's preferences dialogue on macOS, choose Zotero > Preferences… on Windows, it's at the bottom of the Edit menu Select the "Export" tab Either Change the "Default Format" to "Wikipedia Citation Templates"
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projetjourdain.org projetjourdain.org
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Network map of relationships between greek philosophers
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- Sep 2021
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bdj.pensoft.net bdj.pensoft.net
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bioinvasions
This string has been defined as a Wikidata lexeme via https://www.wikidata.org/wiki/Lexeme:L593933.
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- Aug 2021
- Mar 2021
- Feb 2021
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www.uib.no www.uib.no
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www.gbif.org www.gbif.orgSearch1
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www.gbif.org www.gbif.orgSearch1
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www.gbif.org www.gbif.orgSearch1
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www.gbif.org www.gbif.orgSearch1
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www.gbif.org www.gbif.orgDNV GL1
- Nov 2020
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es.wikipedia.org es.wikipedia.org
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[editar datos en Wikidata]
Los datos de esta infobox provienen del Wikidata de Remedios Zafra
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- Oct 2020
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www.mitpressjournals.org www.mitpressjournals.org
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recently released NIH Open Citation Collection,
It may be worth it programming a bot that brings this information to wikidata
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elifesciences.org elifesciences.org
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Relación entre datos y conocimiento.
Waagmeester, A., Stupp, G., Burgstaller-Muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-Rosinach, N., Schriml, L. M., … Su, A. I. (2020). Wikidata as a knowledge graph for the life sciences. eLife, 9, e52614. https://doi.org/10.7554/eLife.52614
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Waagmeester, A., Stupp, G., Burgstaller-Muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-Rosinach, N., Schriml, L. M., … Su, A. I. (2020). Wikidata as a knowledge graph for the life sciences. eLife, 9, e52614. https://doi.org/10.7554/eLife.52614
En este artículo se da la importancia que ha tenido Wikidata para poder organizar información pertinente a genómica, proteómica, compuestos químicos y enfermedades.
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- Apr 2020
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github.com github.com
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Petermr/openVirus. (n.d.). GitHub. Retrieved April 8, 2020, from https://github.com/petermr/openVirus
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- Mar 2020
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larsgw.blogspot.com larsgw.blogspot.com
- Feb 2020
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www.vice.com www.vice.com
- Jul 2019
- Jun 2019
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tools.wmflabs.org tools.wmflabs.org
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- May 2019
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www.goifoundation.org www.goifoundation.org
- Apr 2019
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www.societybyte.swiss www.societybyte.swiss
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www.arl.org www.arl.org
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cen.acs.org cen.acs.org
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Nafion by-product 2
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journal.code4lib.org journal.code4lib.org
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Seized with the desire to improve the visibility of Canadian music in the world, a ragtag band of librarians led by Stacy Allison-Cassin set out to host Wikipedia edit-a-thons in the style of Art+Feminism, but with a focus on addressing Canadian music instead. Along the way, they recognized that Wikidata offered a low-barrier, high-result method of making that data not only visible but reusable as linked open data, and consequently incorporated Wikidata into their edit-a-thons. This is their story.
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- Mar 2019
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www.wired.com www.wired.com
- Feb 2019
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echa.europa.eu echa.europa.eu
- Nov 2018
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www.wikidata.org www.wikidata.org
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Now you know how to search for all works of art, or all buildings, or all human settlements: the magic incantation wdt:P31/wdt:P279*, along with the appropriate class. This uses some more SPARQL features that I haven’t explained yet, but quite honestly, this is almost the only relevant use of those features, so you don’t need to understand how it works in order to use WDQS effectively. If you want to know, I’ll explain it in a bit, but you can also just skip the next section and memorize or copy+paste wdt:P31/wdt:P279* from here when you need it.
wdt:P31/wdt:P279*= magic incantation for Wikidata SPARQL to mean "instance of or subclass of"
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Local file Local file
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Wikidatahas still a lower normative burden of rules and policies than Wikipedia
Hopefully this will not change too fast!
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For the second, we could try to detect inconsistencies, eitherby inspecting samples of the class hierarchy
Yes, that's what I do when doing quality work on the taxonomy (with the tool wdtaxonomy)
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these are not the only reason behindthe trends observed. An examination of the peaks
See http://wikicite.org/statistics.html for similar phases and events better analysed by history instead of calculations.
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Wikidata quality assessment
I guess the the average values are spoiled by outliers. A look at distribution would be interesting instead of average and median value only.
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Ontology depth
I'm curious about the depth distribution to compare my findings on other classification systems, including Wikipedia categories: https://arxiv.org/abs/cs/0604036
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Possible relations between Items
This only includes properties of data-type item?! It should be made more clear because the majority of Wikidata classes has other data types.
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sed in the present analysis
I'd add number of classes with connected Wikipedia articles because these provide definition and context
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and as such not connected to editing activities
Other aspects of Wikidata ontology quality can also be connected to editing activities but this cannot be measure from the Wikidata data dumps. It would need to take into account external data such as applications that make use of Wikidata (Histropedia, Wikipedia instances...)
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A KG typically spans across several domains and is built on topof a conceptual schema, orontology, which defines what types of entities (classes) are allowed inthe graph, alongside the types ofpropertiesthey can have
Wikidata differs from typical KG as it is not build on top of classes (entity types). Any item (entity) can be connected by any property. Wikidata's only strict "classes" in the sense of KG classes are its data types (item, lemma, monolingual string...).
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- Aug 2018
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Collaboration started during April, 2018.
Inception date for the Joint Roadmap for Open Science Tools.
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- May 2018
- Apr 2018
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www.sciencedirect.com www.sciencedirect.com
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[45
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cardiolipin
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phosphatidylserine
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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These findings show that WDR60 mutations can cause skeletal ciliopathies and suggest a role for WDR60 in ciliogenesis.
This is referenced in the Wikidata entry about WDR60 at https://www.wikidata.org/w/index.php?title=Q21124736&oldid=619612847#P682 , which states that WDR60 (Q21124736) is involved in the biological process (P682) of embryonic skeletal system morphogenesis (Q14886895).
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- Aug 2017
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CFD
computational fluid dynamics https://www.wikidata.org/wiki/Q815820
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Adjusted Reelin-positive cell densities were also reduced in CA4 areas of subjects with bipolar disorder (ANOVA, P < 0.001)
Cells immunopositive for reelin are reduced in CA4 hippocampal subfield
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Significant reductions were observed in Reelin-positive adjusted cell densities in the dentate molecular layer (ANOVA, P < 0.001), CA4 area (ANOVA, P < 0.001), total hippocampal area (ANOVA, P < 0.038) and in Reelin-positive cell counts in CA4 (ANOVA, P < 0.042) of schizophrenics vs controls.
Cells immunopositive for reelin are reduced in several hippocampal subfields
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www.wikidata.org www.wikidata.org
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User:Daniel Mietchen/FSCI 2017
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- May 2016
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ia601702.us.archive.org ia601702.us.archive.org
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Sir George Biddell Airy
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- Apr 2016
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www.isb-sib.ch www.isb-sib.ch
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Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.
This is going to be a good talk. Get your coffee, open your eyes, and open your mind! A pattern that could actually scale up - worth a try! Disagree? reply here.
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TextpressoCentral
Could this be used as a front end to adding content to wikidata ?
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docs.google.com docs.google.com
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Below you will find a pretty thorough listing of helpful links for understanding wikidata. Please extend, its openly editable.
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- Feb 2016
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blog.databaseanimals.com blog.databaseanimals.com
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Wikidata, in some sense, turns DBpedia around, in that Wikidata is intended to be a data source to populate Wikipedia infoboxes than the other way around.
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