National agencies support expansion of protein structure database through new initiative
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This document summarizes key points from three separate articles or documents. It discusses the development of subject-specific search engines to more comprehensively index the scientific web. It notes that many scientific pages are never discovered by general search engines. It suggests subject-specific search engines could better index specific domains by using keyword-mounted crawlers to frequently screen last-level pages within a site. The document also discusses two other articles, one addressing efforts by Japan to improve scientific quality and cooperation, and another pointing out that Galileo's drawings of the Moon were quite accurate when compared to modern photographs, contrary to some claims.
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National agencies support expansion of protein structure database through new initiative
- 1. © 1999 Macmillan Magazines Ltd helpedtoorganizeameetingatArgonne NationalLaboratorywhichtriggeredsub- sequentmeetingsatNIHandelsewhere thatresultedinthePSI. AllthreeagenciessupporttheProtein DataBank,whichismanagedbythe ResearchConsortiumforStructuralBio- informaticstoprovideaccesstothemore than10,000knownproteinstructures.The additionof10,000newstructuresthrough thePSIwillprovidetheinformation neededtodefinetheseveralthousandkey proteinfoldsthat,inturn,shouldenable classificationofproteinsintofunctional categories.Thecontributionsofeachof theseagencies(andthoseofseveralnon- federalorganizations)willbeneededto enabletheNIGMSinitiativetosucceed. Marvin Cassman*, Ari Patrinos† *Director, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892-6200, USA †Associate Director for Biological and Environmental Research, Department of Energy, 19901 Germantown Road, Germantown, Maryland 20874-1290, USA frequentlythantheywouldbymoving throughtheentireweb. MikeGardner2 hasrightlysuggestedthat weneedscience-orientedsearchengines withsetsofscientificmetadata,asmetadata arethekeytobettersearching.Together withthatproposal,anapproachsimilarto peer-reviewingofscientificpublications couldbeappliedforcategorizingand evaluatingwebpagesbasedontheir content,qualityandsubject-specificity.It wouldbefeasibletousealgorithmsand rule-basedexpertsystemstocheckcontent- richness,subject-specificityandfreshness- basedcontext-relevancerankingfor retrievedresults. Millionsofdollarsneedtobeinvestedin developingsearchengines.Thisinvestment couldbecost-effectiveifitresultedinan almostzeronoise-to-signalratioandpre- cisebutcomprehensivesubject-relevant hits.Thedevelopmentworkshouldbedone intheacademicsector,butthecompleted searchengineswouldhavecommercial potential,andwouldgeneratemorerevenue thangeneralsearchenginesbecauseoftheir subject-specificity. Developmentofsubject-specificsearch engineswouldsatisfythegrowingdemand forthelatest,precise,value-added,noise- freehitswithahighlevelofsubjectrele- vance.Manysuchsearchenginestogether wouldbeabletoindexmostoftheWorld- WideWeb. Vishwas Chavan Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India 1. Lawrence, S. & Giles, C. L. Nature 400, 107–109 (1999). 2. Gardner, M. Nature 401, 111 (1999). English,whichissurelyanattempttoreach readersabroad. Itisinterestingtolearnthat40percent ofresearcherssubmitpapersonlytoJapan- esepublications,while34.1percentalso submittointernationaljournals.Doesthat meanthat25.9percentonlypublishin overseasjournals?Iftrue,thiswouldshow thattherearemanyinternationallyminded Japaneseresearchers. Youdoagoodjobofpointingoutweak- nessesandimportantgoalsforJapanese research.Butyouromissionofcomparative numbersforelsewhereintheworlddoes notallowreaderstoseetheprobleminits trueproportions.Itcouldevenbethecase thatyourarticlesinadvertently promote prejudicesaboutJapanesescience,which wouldbeunfortunateatatimewhenmany Japaneseresearchteamsarestrivingto attractforeignscientists. Philippe Buhlmann Department of Chemistry, The University of Tokyo, Hongo 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan correspondence 458 NATURE|VOL402|2DECEMBER1999|www.nature.com Search is on for better search engines Sir — Steve Lawrence and C. Lee Giles stated in their Commentary that most of the popular search engines index only about 7–16 per cent of the World-Wide Web1 . This is alarming, as many scientific web pages containing important data may never be discovered. As the web grows it is going to become increasingly difficult for general search engines to give compre- hensive coverage. The answer to the problem could be the development of subject-specific search engines able to cover most of the contents within that subject. Mostcurrentlyavailablesubject- specificlistsandindexesaremaintainedby humans.Manyofthemaremerelycollec- tionsofwebaddressesandlackcontext- basedrelevancerankingandretrievalof resultsinmultivariatecombinations.What isneededaresearchenginesthatcouldtra- versethroughpagesatthelastlevelina subject-specificwebsite.Theywouldbe abletodothisasthenumbersofsuchsites wouldbewithinmanageablelimits. Crawlersorrobotstraversingthroughsuch asubject-specificwebsubsetcouldbuildup acomprehensiveandcompletebankofkey- words.Inturn,suchkeyword-mounted crawlerswouldefficientlyandmorefre- quentlyscreenthelast-levelpageofthesite. Subject-specificsearchengineswould beabletomaintainthefreshnessofthehits, asthecrawlerswouldcheckamanageable numberofspecificwebpagesmore Japan builds bridges to rest of the world Sir — Your Opinion and News article about research in Japan raise an important and timely issue (Nature 401, 309 & 314; 1999). A focus on higher quality rather than quantity of scientific output, and more emphasis on cooperation with researchers abroad, are indeed important goals for Japanese science. But unfortu- nately the articles did not compare the Japanese situation with that elsewhere. Youreport,forexample,that40percent ofresearcherssubmitpapersonlyto Japanesejournals,whichissaidtoreflect insularity.Buthowcanthereaderdraw suchaconclusionwithoutknowing comparablenumbersforothercountries?I wouldnotbesurprisedif40percentof researchersintheUnitedStates,theUnited KingdomorGermanypublishedonlyin nationaljournals.Andyoudidnot mentionthataconsiderablenumberof Japanesejournalspublisharticlesonlyin Galileo had accurate vision of the Moon Sir — Martin Kemp writes that “the details of Galileo’s cratered Moons are difficult to align precisely with actual features”1 . I would like to draw readers’ attention to the work of Ewen Whitaker2 , a selenographer at the University of Arizona. Whitaker reviewed earlier efforts at identifying the features drawn by Galileo, and took special note of the important contributions of Guglielmo Righini, Owen Gingerich and Stillman Drake. He provided side-by-side comparisons of Galileo’s drawings with modern photographs taken at the same lunar phases, and these provide striking support for his contention that Galileo did indeed observe, and record, very accurately. Whitakerhadexaminedthecopperplate engravingsofthefirsteditionofGalileo’s SideriusNunciusandsevenmanuscript images,andhecommentedon“previously unnoticeddifferencesbetweenthemanu- scriptandprintedversionsofSideriusNun- cius...Intheoriginaleditiontheseengrav- ingspresentareasonablywell-executed appearance,butsubsequenteditionsutilize woodcuts,andthequalitydeterioratesvery rapidlytothepointwheretheyarevirtually unrecognizableasMoonimages.Someof thedisparagingremarksmadeaboutthe drawingsundoubtedlystemfromexamina- tionsofthesecruderimages”. M. W. Friedlander Department of Physics, Washington University, St Louis, Missouri 63130, USA 1. Kemp, M. Nature 401, 116 (1999). 2. Whitaker, E. J. Hist. Astron. 9, 155–169 (1978).