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Crossref Wilbanks
 

Crossref Wilbanks

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    Crossref Wilbanks Crossref Wilbanks Presentation Transcript

    • crossref user meeting boston, ma 18 november 2008 john wilbanks creative commons / science commons
    • threadless
    • knowledge gaps process failures transaction costs lost opportunities
    • knowledge gaps process failures transaction costs lost opportunities is the answer more information?
    • knowledge gaps process failures transaction costs lost opportunities
    • knowledge gaps process failures transaction costs lost opportunities is the answer more information? or process innovation?
    • disruptive processes can’t be planned in advance.
    • disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow.
    • disruptive processes can’t be planned in advance. planned innovation tends to be incremental, and slow. ...and not innovative.
    • process change comes more slowly than information product change
    • process change comes more slowly than information product change the knowledge network requires multiple process changes to come into being.
    • 1. stable systems are resistant to process change on multiple levels.
    • IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
    • IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
    • indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
    • the pre-existing system has blocks in place to prevent process disruption.
    • 40 minutes per year
    • nih policy.
    • more staff, please.
    • Dorothea Salo, http://cavlec.yarinareth.net/2008/10/31/miniature-disasters-and-minor-catastrophes/
    • tension between meeting the demands of adding content and providing services
    • copyright + incentives + labor = FAIL
    • 2. reports from the front lines: building a process innovation is really, really hard.
    • “the commons”
    • knowledge rights
    • “digital commons” interoperability low transaction costs law and technology
    • user interface to copyright
    • 140,000,000+ digital objects online under our licenses licenses “ported” to 45+ countries integrated with Google, Yahoo, Firefox, Microsoft Office...
    • Open Access Content
    • “running code”
    • c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
    • creative work?
    • what do these ideas mean in a world of integrated data?
    • +
    • + + + + is it legal? + + + +
    • a protocol, not a license
    • conflicts with the protection instinct
    • conflicts with the protection instinct the protection instinct is sometimes an instinct to protect “freedom”
    • solves the legal problem
    • but not the container problem.
    • building a web for data: the “semantic web”
    • building a web for data: the “semantic web”
    • making computers understand links between documents links to Web page Web page
    • making computers understand relationships between concepts causes drinking coffee feel awake
    • •and junk) (quality control: spam extension •integrity(brand confusion, loss of remix and attribution) •common protocols or to formats (failure to adhere technology) •nature of all Web things...) persistence (the transient
    • (too much work for coffee)
    • (distributed, networked approaches start to look pretty good)
    • web 2.0, science 3.0, what about making Google work better?
    • over 200 years at one paper/day
    • what you want is a list of genes. not a list of documents.
    • Open Source Data Integration
    • a repository of ontologies, namespaces, and integrated databases.
    • Project A Project B Project C A’s name B’s name C’s name for X for X for X A’s version B’s version C’s version of, or info of, or info of, or info about, X about, X about, X
    • Project A Project B Project C common name for X common name common name for X for X shared ‘about’ RDF A’s version of, B’s version C’s version or info about, of, or info of, or info X about, X about, X
    • naming: database records
    • DRD1, 1812 adenylate cyclase activation ADRB2, 154 adenylate cyclase activation ADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway DRD1IP, 50632 dopamine receptor signaling pathway DRD1, 1812 dopamine receptor, adenylate cyclase activating pathway DRD2, 1813 dopamine receptor, adenylate cyclase inhibiting pathway GRM7, 2917 G-protein coupled receptor protein signaling pathway GNG3, 2785 G-protein coupled receptor protein signaling pathway GNG12, 55970 G-protein coupled receptor protein signaling pathway DRD2, 1813 G-protein coupled receptor protein signaling pathway ADRB2, 154 G-protein coupled receptor protein signaling pathway CALM3, 808 G-protein coupled receptor protein signaling pathway HTR2A, 3356 G-protein coupled receptor protein signaling pathway DRD1, 1812 G-protein signaling, coupled to cyclic nucleotide second messenger SSTR5, 6755 G-protein signaling, coupled to cyclic nucleotide second messenger MTNR1A, 4543 G-protein signaling, coupled to cyclic nucleotide second messenger CNR2, 1269 G-protein signaling, coupled to cyclic nucleotide second messenger HTR6, 3362 G-protein signaling, coupled to cyclic nucleotide second messenger GRIK2, 2898 glutamate signaling pathway GRIN1, 2902 glutamate signaling pathway GRIN2A, 2903 glutamate signaling pathway GRIN2B, 2904 glutamate signaling pathway ADAM10, 102 integrin-mediated signaling pathway GRM7, 2917 negative regulation of adenylate cyclase activity LRP1, 4035 negative regulation of Wnt receptor signaling pathway ADAM10, 102 Notch receptor processing ASCL1, 429 Notch signaling pathway HTR2A, 3356 serotonin receptor signaling pathway ADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization) PTPRG, 5793 transmembrane receptor protein tyrosine kinase signaling pathway EPHA4, 2043 transmembrane receptor protein tyrosine kinase signaling pathway NRTN, 4902 transmembrane receptor protein tyrosine kinase signaling pathway CTNND1, 1500 Wnt receptor signaling pathway `
    • e pluribus unum.
    • we can transform complex queries into links prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> Mesh: Pyramidal Neurons prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname where { graph <http://purl.org/commons/hcls/pubmesh> Pubmed: Journal Articles { ?paper ?p mesh:D017966 . ?article sc:identified_by_pmid ?paper. ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. Entrez Gene: Genes ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166} union {?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. GO: Signal Transduction ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} }
    • we can transform complex queries into links http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23%3E%0Aprefix%20rdfs%3A %20%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0Aprefix%20owl%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2002% 2F07%2Fowl%23%3E%0Aprefix%20mesh%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Frecord%2Fmesh%2F%3E%0Aprefix%20sc%3A%20% 3Chttp%3A%2F%2Fpurl.org%2Fscience%2Fowl%2Fsciencecommons%2F%3E%0Aprefix%20ro%3A%20%3Chttp%3A%2F%2Fwww.obofoundry.org%2Fro %2Fro.owl%23%3E%0A%0Aselect%20%3Fgenename%20%3Fprocessname%0Awhere%0A%7B%20%20graph%20%3Chttp%3A%2F%2Fpurl.org% 2Fcommons%2Fhcls%2Fpubmesh%3E%0A%20%20%20%20%20%7B%20%3Fpaper%20%3Fp%20mesh%3AD017966%20.%0A%20%20%20%20%20%20% 20%3Farticle%20sc%3Aidentified_by_pmid%20%3Fpaper.%0A%20%20%20%20%20%20%20%3Fgene%20sc% 3Adescribes_gene_or_gene_product_mentioned_by%20%3Farticle.%0A%20%20%20%20%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F% 2Fpurl.org%2Fcommons%2Fhcls%2Fgoa%3E%0A%20%20%20%20%20%7B%20%3Fprotein%20rdfs%3AsubClassOf%20%3Fres.%0A%20%20%20%20% 20%20%20%3Fres%20owl%3AonProperty%20ro%3Ahas_function.%0A%20%20%20%20%20%20%20%3Fres%20owl%3AsomeValuesFrom%20%3Fres2.% 0A%20%20%20%20%20%20%20%3Fres2%20owl%3AonProperty%20ro%3Arealized_as.%0A%20%20%20%20%20%20%20%3Fres2%20owl% 3AsomeValuesFrom%20%3Fprocess.%0A%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%2Fclassrelations%3E %0A%20%20%20%20%20%7B%7B%3Fprocess%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2Fobo%23part_of%3E%20go%3AGO_0007166%7D% 0A%20%20%20%20%20%20%20union%0A%20%20%20%20%20%20%7B%3Fprocess%20rdfs%3AsubClassOf%20go%3AGO_0007166%20%7D%7D%0A %20%20%20%20%20%20%20%3Fprotein%20rdfs%3AsubClassOf%20%3Fparent.%0A%20%20%20%20%20%20%20%3Fparent%20owl% 3AequivalentClass%20%3Fres3.%0A%20%20%20%20%20%20%20%3Fres3%20owl%3AhasValue%20%3Fgene.%0A%20%20%20%20%20%20%7D%0A% 20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2Fgene%3E%0A%20%20%20%20%20%7B%20%3Fgene%20rdfs%3Alabel%20% 3Fgenename%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%3E%0A%20%20%20%20%20%7B% 20%3Fprocess%20rdfs%3Alabel%20%3Fprocessname%7D%0A%7D&format=&maxrows=50
    • we can transform complex queries into links
    • we can help scholars “remix” queries prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname where { graph <http://purl.org/commons/hcls/pubmesh> mesh:D009369 { ?paper ?p ?article sc:identified_by_pmid ?paper. . Mesh: Cancer ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0006610} union go:GO_0006610 }} {?process rdfs:subClassOf ?protein rdfs:subClassOf ?parent. GO: Ribosomal Protein ?parent owl:equivalentClass ?res3. ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} }
    • we can build a corpus of queries as links
    • we can re-use cultural tools for scholarship
    • 3. collaboration is the essential factor for the knowledge web.
    • exponential content growth
    • our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
    • but if we can work together...
    • that’s what this “collaboration” stuff is all about
    • that’s what this “collaboration” stuff is all about the infrastructure for this is very, very shaky.
    • prefix dc: <http://purl.org/dc/elements/1.1/> prefix skos: <http://www.w3.org/2004/02/skos/core#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix foaf: <http://xmlns.com/foaf/0.1/>
    • what are the odds that the organizations making the namespaces will be here in 50 years? 100 years?
    • conclusion?
    • 1. to crossref? names for use in semantic web
    • doi:10.1007/
    • doi:10.1007/s10067-006-0283-5 or info:doi:10.1007/s10067-006-0283-5
    • doi:10.1007/s10067-006-0283-5 or info:doi:10.1007/s10067-006-0283-5 http://dx.doi.org/10.1007/s10067-006-0283-5
    • 2. to .org? estate planning.
    • put a copy in a dark archive give the keys to trusted 3rd parties
    • free as in speech
    • free as in speech free as in beer
    • free as in speech free as in beer free as in a puppy
    • free as in speech free as in beer Average Cost Of 100 Pound Dog free as in a puppy Over A Year Good Quality Dog Food $70 x 12 = $840 Dog Accessories (collar, leash, etc.) $30 Dog Toys $30 - $50 Vaccines $35 Flea, Tick, & Heartworm Prevention $320 Dog Treats $200 Boarding $100 - $200 (at $15 - $20 a day) Emergency Costs $0 - $2500 or more Total $1375 or much more
    • 3. to .com? services.
    • “In any case, it is clear that a library containing all possible books, arranged at random, is equivalent (as a source of information) to a library containing zero books.” http://en.wikipedia.org/wiki/The_Library_of_Babel
    • thank you wilbanks@creativecommons.org http://sciencecommons.org