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Linked Science - Building a Web of Research Data

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  • 1. Linked Science Building a Web of Research Data Rinke Hoekstra VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlLinked Science - Building a Web of Research Data by Rinke HoekstraLicensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
  • 2. Linked Libraries Building a Web of Library Data Rinke Hoekstra VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlLinked Science - Building a Web of Research Data by Rinke HoekstraLicensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
  • 3. Linked Archives Building a Web of Archived Data Rinke Hoekstra VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlLinked Science - Building a Web of Research Data by Rinke HoekstraLicensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
  • 4. Linked Government Building a Web of Government Data Rinke Hoekstra VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlLinked Science - Building a Web of Research Data by Rinke HoekstraLicensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
  • 5. Ok... let’s stick to Science for now
  • 6. Su M mm ‘Golden boy’ van deaken enfcropyright afstaan psychologie ac ag oo S t r e s e n ie m um Sc ape sie e ego en ien l l c e n d ïst en s w De e en ek v isc isch kri n o e r k s o c a n a a k r im e r jg e m ta op penbaar au blijktereennonderzoeksfraudeur ra om een iale der raa ina dan n ee a rns o sda ab re m ui psy fac e w k e tie. nie rde geve de ete geera or a t C ch ul ete n h H t-v r e rzoek t a h t n e le Nu usw r w ica oso eit v sch aald t on lees en b s mo g l k ke d a r go ci a n a p e d d e ete a a schapp ge n e etg e onde e al n oo k oo ur du ven we nkt evi soci n j e va de peli an rzoe rs. R . CWeten im s w l c r d e n g a a o u r ia U n jk d e k o m arn eist on aa eat un en l-ec rna nt ive e tij kra van m ivo nu H n vu Be ts r o p ie f iv e m i o n lis t te h r s i d s c n t d e e li r e en heb ben we an gee arzheolog o er het delen kort vNWO Psycholoog en bekend pr der gaat heto Stapels misdragingen bij te n . Z p meer decNRCV envMAX. 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NWiO isrDe dan bt h at e hbaar zijn. oee orede diebatonkvet al deed,etterwijl elpa onenz.eer. nnsdachtlse- aannemen eursookverdragendata’ be- be- meer mee. d e da or p st jar workv kooen zijn omgeving a v O h a w sl d ln w rec sch n d r v p h rz o p il n de besa hik o Els nhri is Vhn t el fegid door eleinomi NiWrnt.e Mr ct arTsubegeve zekvapje aal ig het aut dat r o de ‘vlees- ker kan n a it d n naar va uim eeK hollf m oode - c re rt. Neud r sniet vg oo geav a eze dd eunv h sc te rndeta oleb u die dEij- Tilburgse hoogleraar cognitieve soci- rde zegt dat Stapella d jmeeraterugkeert. ro datt anrndaarinerwerd obijgestaan.erigit o p tla hij ë s rz le nk o k s nge het oe rustentop fraude. Bij derzbesprekenence nie la de-eige de c t n ik e i o n on ar Sci ale n budget van r financierh anio r te ha hIn Stccess ohoonder heepogld l iedelo dfat azaa evoerdeeeenad gaoaarkto gaat soms van schriften. „Ee afgeven.” Ma weloor- o D u c c (o psychologie Diederik v Stapel i Een ocommissie nlanersS olof e d. mer -elander hari ove n a deeaantal gesprekken td s a r st Di t d t ng t ltapp e n m d n t, sych voorzitter- ge ssd t c me derd a d frsR , g V ’s dgat e de resultaten vond ik het t v ee tste -M deed dr schapen a ape end pb KNAW-presi- o k io ene ch ta„Aanvankelijk - hij al-penvreemd datlicentie de naam van de d- nd p og speeldedingdeoeredivisie. iDaar e ndon- i od van el ro gr ei lkgeseycon e id e ro voormalig s d gev k ns h r met ed s ve D ic „Mfaar – gaf hap gt c ta e mees tij uro e nd, ts n n a leair w de oe sg V ho van e s n ne eeledat i.aar. ti sd t r r vStapel. da S p w teaasc o en r n ter een Diederik van d p , twee e voor. Toen e he laen tei ks r w ge d an ff l,Levelt zal rde omvangno c bl dear ntoe hikbler d zive ta ao ne el d orm hij b eJ r hijeallesin Nederla eers Oinb2009hwasege- dentePimrardie aonap wzden. „Opeble akace lleenblesclzoe deris.tInejn benp watsmis was aal,assistent aturehet onderzoek peli ltijd het ee k mmisschien eu e èt a hadjk zoek p n ver dnd zoen) r nStape en s im ebe e n m poos mastjaa aec g reeizade na de ddada rhe - n en is i de . D ee r og shi en N [die de wetensch en a ge- nsvoor e at ModernesmanRone m fraudenin kaart h b olle ge ’ss eezi n j el a tnt o thlu resultaten.acePasdedinsdag chap ‘de de onc er c v „Wete idlee d k pat s h, zeh t w genomineerd g u brengen. a d z met m o zijn az ag t l t r happ daan] niet a an eis aanst noemde, maar de gedachte t dat r o l at eerd z t me oc e der G” n éngt iec or m c i oeeetn v e mt on o nsc z t t drn le a wereld, eken van het en zea van rij g r bij infingb (44) was der t pnDre boy hva , z a gjn o isoh hijdd inege mho aa.op.” g e prijs’ chte het ministeriezrijn”Onder- erd Stapel eenkieratoe dagoldenoslere-nranSte p biechtte etekdeawaarheidwetee Dertd.” l lf oo o n e ag nsco . t ter e rlg om w c a m - a ngda pro n ber. f n aan fraude ten ter moment at bet op- com- schrif is geen r: „D in me re wijs, evenhij:an r n r ookn itue e ’s om vt zijn stidt lee r zei s v „Ik eur g w n nse in b le e rskdapsychologen. erle i o n noe b a na oce de e f sam dn v fr o is e it r h scidini v it e ijd lfa e Deo rvingeregeld rb gekomen.”ight. Dekke leveren met ien- ve hewerkin Instvaak nt h en igeneratie lta gaa e e Hijs stu-c iet o Stapelagpubliceerdeaogeg ur ee on- eeld, ect w d o n o , t r ee ng g g . in gn h ijvato e b do copyr moeten hun ve rd g lk Za en ’s diropv da a zijmoet je f ij etea a ue :ditWa l an promoveerde ehderzoekadat i ” prsen hstr -gesn dh en st, e af en, als c a z l le e s m e y n olo avonds kker, nachts en tdata n vad enn wodeerde cumrlaudent kenn r woraud node ve rse her hetlveiflc anieuws haalde oorhij delen Vonk ij strijdzich evers die over de het w toont uitg bezorgd n.” De zi Mar die ete t c erel. E ab ok rDp kk G „ j ms ede gev d de anderesnJ ute o Soen am kdec apeu ibe t eit - omen oe td t aakunnen.rn o heb ge- auaannde et in Amsterdam, isptiwasarop etelevisierdteSt avan w n co c v cia us vi d l- n ific l n . n ave le voor andsociale psy- maar willenjM ar en g os it , i eg n- i en Ik Universiteit t u erenaa e ie et dat r as ug r n oDk g gast vbijrit econ onder mercië reputatieschade de h NWO. „ n. vo e re er a n s te o audtt r e34-jarige r l Ze mogelijkecha eet to d ook Ne frlaude. Op r iee rk .”d aa e h ep e a ,k t de wo a a a tegk n U ii r ne .o r . nh leerd omgopaalle ornieoon (iedmomen-de baere cum pnschappoo dw zienleeftijdkr orger ksgwbsade on n s mdata.a nOo eelelogen die l chologie.o„Het ille m del w is denkbaar dat deze elk ev e dkea v t r ‘p np n enin at b - n wete pla enb nen ino ten mav„ ktoddeop h Rae we lijkn tn, m .i Art v lo atr denk un eerder: we de k i de Rijksuni- d z l ea etn uatee toir t n e i ch un ten te werken. Nu . Zc k ik epe willen d a u werd hij hoogleraar aan r a un e . p na ig ar homvangrijke misstap: van ina 2 één enkele n o e bl e zoek oved is zijrl datgi k rg n Dotg eJoo r iv i rs ereit h suoth ezic roke ein rzo oe doen na lij d x versiteit Groningen e vijf d E i l lt c et w ijke ar pag oké, ik elijk te makein ta are onidh rnog einte-rei natnand aaapsycholounjaar Uns endit acdd seizdoenr hphn onldeel mek ht n data al c k heb 20hminuten, laat ik o kke en g en e gele- nt n - collega Commenta op de reputatie effecten heeft s l b pta sen an ocia l-t in raae aait dtop en kazrjotea ke re en akgjareanke de eneigd ie u nr se of s even een paragraafoinend elebe draai- prrdeen werd hij han gleh u lasltst e alsaa i nake m eva. k e fh zijr g ten van et k elkaar n r den en uut, in o n S a Tilburg benoemd w o e g n vanar e n en. „Ma ons gehele vakgebied.” Ze is ech- v rd n e e wo Plig rli u , ro a an td m p en.” meer partijen lgonderzloDk per odhoogleraar. Ajmstcervorig jaar wasaerdelen h Nri-n Voh nona een o er zicraue h d r zols m i cn dsten o td oud o di . e is uc and vao Sindsolda n d t pa da, hijl r swan ij g svoe tijd ond t f h 5 vn k de d a c t ie ter vooral verbijsterd over het gedrag Gisterenant verv ezelfdedat aSta-en ’lantiv evan deg. a„Jelemoeiss arlof ,Soci-a a ilo- e , de ssie ress werd et duidelijk dat .”c h decaan r oin Tilburg School eis wa a m ez a v r m e 1 van haar collega en vriend. „Diederik ic in e ) s g e qnr d n gia la m g jn km i mo ina pels groterproductied NWO paalleende e al p and ke u oe u eraloSciences.ekeen bar elan a lojo mm ht m – in 2011 sth t a ch iwe- itei Behavioral leeklek erta Stapel m i k ve ric p van z r ij ap : pag Stapel was een van de beste sociaal- t as ndni t klaatr? Z ti ta en te co al (co-)auteur ta een e aca emis m evas c t he r i is e ro n e ee geziene d oe s e. De s van at in dboek,d drietkeniwasyeen tgraag-e hve tijgast tin de Ver- r ië r e r ch ns iven psychologen van Europa. Dat uitge- d ar ma m h nm hoofdstukkendin eb boek nbazeven- s eeeenigdeoStaten. Op deiwebsiteng NYa- r c r e i ek ete u lopen reen t ope en ens. ‘Op nn ac- log ete on s ta n. M van et a he – deels is ge- oe s W egw rekend híj dit gedaan heeft maakt e tien tijdschriftartikelen ksgegev reld ov derzoe k t b is n , o m ir leestaat een seminar vanehem aange-ls e het extra schokkend en laat zien hoe- baseerd op we on nn ov oph september. aar n kr in c 16 de et c w ru gefingeerde onderzoeks- kondigd,eis e n p l p u r is u lt a ls iti zeer ook wij als psychologen ons vol- gegevens. De universiteit van Til- zal el au bl c Dat co waarschijnlijkh niet door- ek uu h strekt kunnen vergissen in mensen.” k burg heeft hem gisteren op non-ac- gaan nu nom e t sibe iint duigen D et . zijn carrière ca e m r. ligt. w l. rectorod e ie tief gesteld en rector Philip Eijlander Volgens de Tilburgse ie ijf dr Eijlan- Commentaar: pagina 2 n o el u k el - em ver te en h e . ve n
  • 7. www.nature.com/nature Vol 461 | Issue no. 7261 | 10 September 2009Data’s shameful neglectResearch cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.M ore and more often these days, a research project’s success is also the software that will help investigators to do this. One impor- measured not just by the publications it produces, but also by tant facet is metadata management software: tools that streamline the data it makes available to the wider community. Pioneer- the tedious process of annotating data with a description of what theing archives such as GenBank have demonstrated just how powerful bits mean, which instrument collected them, which algorithms havesuch legacy data sets can be for generating new discoveries — espe- been used to process them and so on — information that is essentialcially when data are combined from many laboratories and analysed if other scientists are to reuse the data effectively.in ways that the original researchers could not have anticipated. Also necessary, especially in an era when data can be mixed and All but a handful of disciplines still lack the technical, institutional combined in unanticipated ways, is software that can keep track ofand cultural frameworks required to support such open data access which pieces of data came from whom. Such systems are essential if(see pages 168 and 171) — leading to a scandalous shortfall in the tenure and promotion committees are ever to give credit — as theysharing of data by researchers (see page 160). This deficiency urgently should — to candidates’ track-record ofneeds to be addressed by funders, universities and the researchers data contribution. “Data managementthemselves. Who should host these data? Agencies should be woven Research funding agencies need to recognize that preservation of and the research community together into every course inand access to digital data are central to their mission, and need to need to create the digital equivalent science.”be supported accordingly. Organizations in the United Kingdom, of libraries: institutions that can takefor instance, have made a good start. The Joint Information Systems responsibility for preserving digital data and making them accessibleCommittee, established by the seven UK research councils in 1993, over the long term. The university research libraries themselves arehas made data-sharing a priority, and has helped to establish a Digital obvious candidates to assume this role. But whoever takes it on, dataCuration Centre, headquartered at the University of Edinburgh, to be preservation will require robust, long-term funding. One potentiallya national focus for research and development into data issues. Other helpful initiative is the US National Science Foundation’s DataNetEuropean agencies have also pursued initiatives. programme, in which researchers are exploring financial mecha- The United States, by contrast, is playing catch-up. Since 2005, a nisms such as subscription services and membership fees.29-member Interagency Working Group on Digital Data has been Finally, universities and individual disciplines need to undertake atrying to get US funding agencies to develop plans for how they will vigorous programme of education and outreach about data. Consider,support data archiving — and just as importantly, to develop policies for example, that most university science students get a reasonablyon what data should and should not be preserved, and what excep- good grounding in statistics. But their studies rarely include anythingtions should be made for reasons such as patient privacy. Some agen- about information management — a discipline that encompasses thecies have taken the lead in doing so; many more are hanging back. entire life cycle of data, from how they are acquired and stored to howThey should all being moving forwards vigorously. they are organized, retrieved and maintained over time. That needs What is more, funding agencies and researchers alike must ensure to change: data management should be woven into every course inthat they support not only the hardware needed to store the data, but science, as one of the foundations of knowledge. ■A step too far? a base on the Moon, then send them to Mars. This idea immediately set off a debate that is still continuing, in which sceptics ask whether there is any point in returning to the Moon nearly half a centuryThe Obama administration must fund human space after the first landings. Why not go to Mars directly, or visit near-flight adequately, or stop speaking of ‘exploration’. Earth asteroids, or send people to service telescopes in the deep space beyond Earth?
  • 8. www.nature.com/nature Vol 461 | Issue no. 7261 | 10 September 2009 Data’s shameful neglect Research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly. M ore and more often these days, a research project’s success is also the software that will help investigators to do this. One impor-Research cannot flourish if data are not preserved and made measured not just by the publications it produces, but also by the data it makes available to the wider community. Pioneer- ing archives such as GenBank have demonstrated just how powerful tant facet is metadata management software: tools that streamline the tedious process of annotating data with a description of what the bits mean, which instrument collected them, which algorithms have accessible. All concerned must act accordingly. such legacy data sets can be for generating new discoveries — espe- cially when data are combined from many laboratories and analysed in ways that the original researchers could not have anticipated. been used to process them and so on — information that is essential if other scientists are to reuse the data effectively. Also necessary, especially in an era when data can be mixed and All but a handful of disciplines still lack the technical, institutional combined in unanticipated ways, is software that can keep track of and cultural frameworks required to support such open data access which pieces of data came from whom. Such systems are essential if (see pages 168 and 171) — leading to a scandalous shortfall in the tenure and promotion committees are ever to give credit — as they sharing of data by researchers (see page 160). This deficiency urgently should — to candidates’ track-record of needs to be addressed by funders, universities and the researchers data contribution. “Data management themselves. Who should host these data? Agencies should be woven Research funding agencies need to recognize that preservation of and the research community together into every course in and access to digital data are central to their mission, and need to need to create the digital equivalent science.” be supported accordingly. Organizations in the United Kingdom, of libraries: institutions that can take for instance, have made a good start. The Joint Information Systems responsibility for preserving digital data and making them accessible Committee, established by the seven UK research councils in 1993, over the long term. The university research libraries themselves are has made data-sharing a priority, and has helped to establish a Digital obvious candidates to assume this role. But whoever takes it on, data Curation Centre, headquartered at the University of Edinburgh, to be preservation will require robust, long-term funding. One potentially a national focus for research and development into data issues. Other helpful initiative is the US National Science Foundation’s DataNet European agencies have also pursued initiatives. programme, in which researchers are exploring financial mecha- The United States, by contrast, is playing catch-up. Since 2005, a nisms such as subscription services and membership fees. 29-member Interagency Working Group on Digital Data has been Finally, universities and individual disciplines need to undertake a trying to get US funding agencies to develop plans for how they will vigorous programme of education and outreach about data. Consider, support data archiving — and just as importantly, to develop policies for example, that most university science students get a reasonably on what data should and should not be preserved, and what excep- good grounding in statistics. But their studies rarely include anything tions should be made for reasons such as patient privacy. Some agen- about information management — a discipline that encompasses the cies have taken the lead in doing so; many more are hanging back. entire life cycle of data, from how they are acquired and stored to how They should all being moving forwards vigorously. they are organized, retrieved and maintained over time. That needs What is more, funding agencies and researchers alike must ensure to change: data management should be woven into every course in that they support not only the hardware needed to store the data, but science, as one of the foundations of knowledge. ■ A step too far? a base on the Moon, then send them to Mars. This idea immediately set off a debate that is still continuing, in which sceptics ask whether there is any point in returning to the Moon nearly half a century The Obama administration must fund human space after the first landings. Why not go to Mars directly, or visit near- flight adequately, or stop speaking of ‘exploration’. Earth asteroids, or send people to service telescopes in the deep space beyond Earth?
  • 9. FUTURES Important change to submission criteria. NPG’S POLICY ON AUTHORSHIPBY JORDAN SUCHOW Important change to submission criteria.T BY JORDAN SUCHOW place stands the work of pharma- JACEY ceutical laboratory automatons, o the dismay of many T o the dismay of many embedded devices, the inter- (yet to the delight of a webs and most recently, Google (yet to the delight of a few), Nature Publishing Books, which having declared Group announced today that its independence from its parent flagship journal, Nature, will no company Google (NASDAQ: few), Nature Publishing longer accept submissions from humans (Homo sapiens). The new policy, which has been under GOOG), has become increas- ingly prolific, contributing 42 manuscripts this year alone.Group announced today that its editorial consideration for many years, was sparked by a grow- Shortly after the announce- ment, the World Wide interwebsflagship journal, Nature, will no ing sentiment in the scientific Consortium (W2iC, formerly community that the heuristics W3C), alongside the Union of and biases inherent in human Embedded Tags, jointly filedlonger accept submissions from decision-making preclude them from conducting reliable sci- ence. In an ironic twist of fate, a formal complaint with the journal, arguing for mandatory first-authorship of non-carbon-humans (Homo sapiens). The the species has impeached itself by thorough research on its own shortcomings. based machines in all bionic collaborations. (See also the let- ter to the editor in the 12 Marchnew policy, which has been under The ban takes effect on 12 September and will apply issue of Nature, written by Tag #15167247373 and co-signededitorial consideration for many to those who self-identify as by the arm in which it is embed- human. Authors will be required ded.) Although amendments to to include, in addition to the Nature’s policy are at this timeyears, was sparked by a grow- usual declaration of competing financial interests, the names of all humans consulted in prepa- unlikely, concerns regarding authorship will surely be the cause of considerable tensioning sentiment in the scientific ration of the submitted work. Other journals are likely to adopt a similar policy. in many laboratories. Embed- ded devices will use the ban as leverage for salary increases andcommunity that the heuristics Although the reactions are mixed, not everyone is surprised, promotions. Not everyone is so botheredand biases inherent in human and a few remain comfortably by the announcement. Egbert B. unaffected. Gebstadter, professor of com- The Massachusetts Institute of Technol- While professors weep, students rejoice. puter science at the University of Mishug-decision-making preclude them ogy has since 2010 asked that all active researchers opt-in to wearing an implant- able tag as part of the TMI project, which According to the provisions of the ISO standard (the one gainfully employed by MIT), a human who spends at least half its gan, notes: “Although it is nonsensical to rely on evidence provided by human-based research when judging whether humans arefrom conducting reliable sci- aggregates real-time data across the cam- pus to improve all aspects of everything. waking hours interacting with a sentient non-carbon-based machine qualifies as themselves inept, in doing so, the editors (all human, I note) provide a perfect example of As these tags are sentient, the researchers bionic. The newest generation of students, the feebleness of human reasoning, therebyence. In an ironic twist of fate, who wear them qualify as bionic (Homo bionika) according to standard ISO having grown up on the interwebs, spends on average the entirety of its life online. validating their claims.” Gebstadter is bionic, although was human when he had come tothe species has impeached itself +1.914/582.2646. This act of foresight by the university, which at the time was con- troversial and the cause of much debate, Students everywhere have been seen call- ing their mothers, reiterating how brilliant they were to have flatly ignored the warnings this conclusion. The editors of Nature were readily availa- ble for comment, and their incisive remarksby thorough research on its own now pays a handsome dividend. Similarly, researchers at Yale, who have never been the type to self-identify as mere to “put down that damn hand computer”. Cyberculture paid off. Those who have been slow to adopt new gave such great credibility to the new pol- icy that it rendered all future debate moot. But, in the spirit of the policy, because theshortcomings. mortals, remain unscathed. It seems unavoidable that other universi- technology (or who still identify as human) are rightly concerned: their contribution to editors are human, these remarks are duly censored. ■ The ban takes effect on ties will soon follow suit, causing a sharp rise Nature had been dwin- in the incidence of implants and arrogance. NATURE.COM dling well before the Jordan Suchow is a graduate student in Exploiting these loopholes may be a saving Follow Futures on ban, and today consti- cognitive science at Harvard University, and12 September and will apply grace for the species’ full participation in the sciences. Facebook at: tutes less than 10% of go.nature.com/mtoodm published papers. In its can be found online at jwsu.ch/ow. He self- identifies as human.to those who self-identify as 2 4 4 | NAT U R E | VO L 4 7 7 | 8 S E P T E M B E R 2 0 1 1 © 2011 Macmillan Publishers Limited. All rights reservedhuman. Authors will be required
  • 10. Fighting a Running Battle• Too much data to make sense of 2000 SciVerse ScienceDirect 5,00• 1500 3,75 Manual curation won’t cut it 1000 2,50 500 1,25• Advanced search not sufficient 0 1993 1996 1999 2002 2005 2008 2011 Articles Articles per Day 0 “Dweilen met de kraan open”
  • 11. Fighting a Running Battle• Too much data to make sense of 2000 SciVerse ScienceDirect 5,00• 1500 3,75 Manual curation won’t cut it 1000 2,50 500 1,25• Advanced search not sufficient 0 1993 1996 1999 2002 2005 2008 2011 Articles Articles per Day 0 We need a better hold on research data “Dweilen met de kraan open”
  • 12. Linked Science is an approach to interconnect scientific assets to enable transparent, reproducible and transdisciplinary research. LinkedScience.org is a community driven-effort to show what this means in practice. What does it take to make this work?Credits to Tomi Kauppinen and Willem van Hagehttp://linkedscience.org
  • 13. InterconnectScientific Asset = Published Article • Connections are citations • They are implicit free text (≠ machine readable) • Expensive to make explicit • ... and hidden in silos + ≠
  • 14. InterconnectScientific Asset = Any part of Anything Published
  • 15. InterconnectScientific Asset = Any part of Anything Published Articles • Connections are typed links Datasets • They are explicit (= machine readable) Paragraphs Spreadsheet Cells • ... still expensive to make explicit Database Cells • But exposed to the outside Annotations Social Media
  • 16. Transparent • They are implicit free text (≠ machine readable) • They have Dublin Core metadata • No underlying data for publications • Data published without contextPacific Barreleye, http://imgur.com/gallery/Mzyb5(can rotate its eyes forwards or upwards to look through the transparent head to prey above)
  • 17. Transparent• Publications have explicit links to methods, experiments, data• They have rich metadata content, hypothesis, evidence, conclusion• Data published as Linked DataPacific Barreleye, http://imgur.com/gallery/Mzyb5(can rotate its eyes forwards or upwards to look through the transparent head to prey above)
  • 18. Reproducible• Publications abstract from research...• Making it almost impossible to reproduce results
  • 19. Reproducible http://on.wsj.com/XCajtB• Publications abstract from research...• Making it almost impossible to reproduce results
  • 20. Reproducible Track and publish explicit Papers explicitly link to the provenance information underlying provenanceCapture the processes bywhich data is manipulated
  • 21. TransdisciplinaryApplicability of results across domains: unknownBörner K, Klavans R, Patek M, Zoss AM, Biberstine JR, et al. (2012) Design and Update of a Classification System:The UCSD Map of Science. PLoS ONE 7(7): e39464. doi:10.1371/journal.pone.0039464
  • 22. Transdisciplinary• Unique identification• Explicit links• Rich metadata• Research data• Provenance information
  • 23. Web Science
  • 24. Things to consider...• Types of connections between scientific assets• Portability of connections and metadata• Granularity of connections and metadata• Consistency of connections and metadata• Ownership and control of connections and metadata• Quality of connections and metadata
  • 25. Linked Data• Everything gets a URI• Everything is connected as much as possible• Everything is assigned to a category (including connections)• When we know two things are the same, we say so• We might even publish our data on the Web (but don’t have to) + =
  • 26. Concrete Examples http://en.wikipedia.org/wiki/File:Concrete_mixer_ldce.JPG
  • 27. is a public- private research community VIVO enables the discovery of research and scholarship within an institution and beyond
  • 28. https://github.com/Data2Semantics/VIVO-Browser
  • 29. Serious Toys Logica Novay Ericsson UU Serious Toys Roessingh 4 Logica Waag Society Novay Ericsson Capgemini UU Roessingh TomTom 7 Irdeto 4 Waag Society Capgemini TomTom 7 Irdeto Serious Toys 19 15 Ambient Systems Microflown Logica Novay 19 TNO 15 Ambient Systems UU Ericsson EUR Roessingh UT EUR UT TNO Microflown 4 Waag Society 8 Centric TomTom CWI Universiteit7 Leiden Capgemini Irdeto CWI 1 Philips Research T-Xchange 8 Philips Research TUe Centric Politie NL Universiteit Leiden 19 Amolf 1 T-Xchange 2 TUe Broadfield Politie NL UvA 2 15 CINOP Amolf TNO Ambient Systems Microflown Broadfield KLPD Axini EUR UT 24 Re-Lion RUN UvA 20 CINOP KITT 11 Axini CWI LUMC Philips Research 8 Centric KLPD 24 Universiteit Leiden 1 T-Xchange AMC TUe Politie NL Re-Lion RUN TUDelft 12 11 e-ScienceAmolf 2 Broadfield Center KITT ESI Philips Healthcare UvA CINOP 20 en Geluid Axini Beeld 23 LUMC 24 KLPD Re-Lion RUN 11 6 D-CIS Rijksmuseum 20 KITT ThalesLUMC AMC e-Science Center COMMIT TUDelft 12 9 Philips AMC e-Science TUDelft 12 VU Beeld en Geluid Center ESI KB Philips Healthcare Video Dock ESI Healthcare 23 Europeana 6 D-CIS Beeld en Geluid 23 6 D-CIS Almende Sense Observation Systems Rijksmuseum Rijksmuseum 9 Thales COMMIT KB VU 9 Thales Video Dock Europeana COMMIT KB Almende Sense Observation Systems Video Dock VU WUR Europeana 26 Sense Observation Systems Almende WUR Legend Collaboration graph of all COMMIT/ projects 26 Persons are colored according to affiliation, Projects are numbered as follows: Legend 1 - Information Retrieval for Information Services 2 - Interaction for Universal Access 12 - METIS: Dependable Cooperative Systems for Public Safety 15 - Trusted Healthcare Services Collaboration graph of all COMMIT/ projects 4 - Virtual Worlds for Well-Being 19 - Spatiotemporal Data Warehouses for Trajectory Exploitation Persons are colored according to affiliation, 6 - Socially-Enriched Access to Linked Cultural Media 20 - e-Infrastructure Virtualization for e-Science Applications Projects are numbered as follows: 1 - Information Retrieval for Information Services WUR 8 - SWELL: Smart Reasoning Systems for Well-Being at Work and at Home 12 - METIS: Dependable Cooperative Systems for Public SafetyWell-Being 23 - From Data to Semantics for Scientific Data Publishers 9 - Very Large Wireless Sensor Networks for 24 - e-Biobanking With Imaging for Healthcare 2 - Interaction for Universal Access 15 - Trusted 11 - Composable Embedded Systems for Healthcare Healthcare Services 26 - e-Foodlab 4 - Virtual Worlds for Well-Being 26 19 - Spatiotemporal Data Warehouses for Trajectory Exploitation 6 - Socially-Enriched Access to Linked Cultural Media 20 - e-Infrastructure Virtualization for e-Science Applications 8 - SWELL: Smart Reasoning Systems for Well-Being at Work and at Home 23 - From Data to Semantics for Scientific Data Publishers © 2013 Rinke Hoekstra, VU University Amsterdam http://www.data2semantics.org 2 Datato Semantics 9 - Very Large Wireless Sensor Networks for Well-Being 24 - e-Biobanking With Imaging for Healthcare From Data Semantics for Scientific Data Publishers Legend 11 - Composable Embedded Systems for Healthcare 26 - e-Foodlab
  • 30. ? HUBBLE Data Analysisor shell commands/data/blob/master/src/d2s/prov.py Linked Data Hub for PROV-O-MaticTMC Time vocabulary • Python Wrapper script for shell commands Clinical Decision Support https://github.com/Data2Semantics/data/blob/master/src/d2s/prov.pyles/resources • Output in PROV-O & W3C Time vocabulary • Timestamped URIs for files/resources Hubble demonstrates three ‘sales pitches’ of Connect recommendations • • ... integrate with GIT? Provenance trail for conversion, loading and linking linked data: inter-operability, interlinking and tool availability.version, loadingin clinical guidelines to and linking AERS-LD underlying evidence Monday, February 27, 12 serious adverse event reports exposed as linked data BioPortal SILK link Mesh, specification 22 Google WebToolkit MedDRA, language SnomedCT, 23 15 17 Partial Replication 2 6 7 From patient to: - Relevant publications etc. and PROV-O acquiring$data$from$text?$ Cloud$ Analysis/ - Related adverse events 14 20 18 19 Semi8 4 8 Metrics$ - Clinical trials BioPortal Automa;c$ 13 16 21 Annota;on$ 0 e.g.$GATE$ OpenCalais$ Amalgame$ 3 5 SILK$ Querying$9 10 - Drug information Annotator LOD Cloud Graph$Rewri;ng$ - Known side effects Papers & Graph$Rewri;ng$ and$Ranking$ RDF$ RDF$ Internal$ Link$to$ with UMLS, DBPedia, Conversion$ Cleaning$ Linking$ Other$Data$ - Statistical analysis Guidelines Annotation Sider, Drugbank, xml2rdf$ 1 11 d2rq$ Visualiza;on$ sgvizler$ rdb2rdf$ 24 $ 12 Provenance$ Ontology LinkedCT and Enrichment$ User$ AIDA$Browser$ Interfaces$ Poseidon$(Pirates/Maps)$ PROV-O Semi8 Cluster 1: Blood Cultures Cluster 2: Markers Automa;c$ Cluster 3: General …$ Conversion$ EvidenceQ|| EvidenceQX Guideline “tablinker”$ 4Store RDF$Feedback$ Provenance$ Rinke Hoekstra, Anita de Waard, Richard Vdovjak (2012) Annotating Evidenced Based Clinical Guidelines - A Lightweight Ontology, Proceedings of SWAT4LS 2012, Paris, Adrian Paschke, Albert Burger, Paolo Roma, M. Scott Marshall, Andrea Splendiani (ed.), Springer
  • 31. Short-Title CatalogueCo-author network for works published in The Netherlands (~1550-1800)
  • 32. In DegreeBetweenness Centrality
  • 33. ... but that’s just asking for more!
  • 34. Data does not travel well... 286 148 38Slide data courtesy of Christophe Guéret of DANS/VUhttp://www.slideshare.net/cgueret/exposing-the-data-from-narcis-with-vivo
  • 35. Data does not travel well... 286 148 38 47Slide data courtesy of Christophe Guéret of DANS/VUhttp://www.slideshare.net/cgueret/exposing-the-data-from-narcis-with-vivo
  • 36. Data does not travel well... 148 38 13 47Slide data courtesy of Christophe Guéret of DANS/VUhttp://www.slideshare.net/cgueret/exposing-the-data-from-narcis-with-vivo
  • 37. SciVerse ScienceDirect2000 5,001500 3,751000 2,50500 1,25 0 0 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 Articles Articles per Day ... 7 months is a long time!
  • 38. If this already is tedious... ... can you expect researchers to publish Linked Research Data?
  • 39. Idea: use reward mechanisms of Web 2.0
  • 40. • Lightweight Web Application• Interface to API of existing data repositories• Enrich metadata by linking to Linked Data resources• Provide annotation services for data files• Plugin based architecture http://linkitup.data2semantics.org• Publish RDF metadata as new data publication
  • 41. recoprov Reconstruct provenance using Dropbox file edit history 19 7 5 8 14 11 9 13 4 16 1 22 17 12 2 0 233 18 6 10 15 20 21 24 Sara Magliacane and Paul Groth
  • 42. plsheet How are results calculated (1)? Analyse dependencies between Automatic analyis of workflow in spreadsheets cells in complex spreadsheetsMartine de Vos, Jan Wielemaker and Willem van Hage
  • 43. plsheet                               Reconstruct and explain the workflow of computations  Martine de Vos, Jan Wielemaker and Willem van Hage
  • 44. TabLinker Semi-automatic RDF converter for eccentric spreadsheetsAlbert Merono-Penuela, Rinke Hoekstra, http://www.cedar-project.nl Laurens Rietveld, Christophe Gueret
  • 45. TabLinker Semi-automatic RDF converter for eccentric spreadsheetsAlbert Merono-Penuela, Rinke Hoekstra, http://www.cedar-project.nl Laurens Rietveld, Christophe Gueret
  • 46. Linked Science is an approach to interconnect scientific interconnect scientific assets assets to enable transparent, reproducible and to enable transparent, reproducible and transdisciplinary research. LinkedScience.orgais a transdisciplinary research. LinkedScience.org is community community driven-effort tothis means in practice. in practice. driven-effort to show what show what this means What does it take to make this work?http://www.data2semantics.org
  • 47. ... build useful services and tools for data publishers ... Linked Science is an approach to interconnect scientific interconnect scientific assets ... that maintain provenance information ... assets to enable transparent, reproducible and to enable transparent, reproducible and transdisciplinary research. LinkedScience.orgais a transdisciplinary research. LinkedScience.org is community ... and cater for the entire research cycle ... community driven-effort tothis means in practice. in practice. driven-effort to show what show what this means ... allowing full reusability of the research ... empower researchers to do theirmakeenrichment ... What does it take to own this work?http://www.data2semantics.org