Hands-on Activity 7: Metadata - GitHub Pages...This is some (fictional) information about the...
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Hands-on Exercises for Data Management http://www.dataone.org/education-modules 1 Hands-on Activity 7: Metadata Associated DataONE Lecture: Lesson 7: Metadata Objectives: Students consider the level of detail that is necessary for metadata to adequately describe data sets, and work with a metadata record. Outcomes: (1) Students can explain why detailed metadata are valuable. (2) Students can provide suggestions for improving metadata descriptions. Time Needed: 45 minutes in class. URLs: Morpho (https://knb.ecoinformatics.org/#tools/morpho), DataUp (http://dataup.cdlib.org/) Additional Files Needed: xlsx, zoop- temp-main.xlsx; zoop-temp.xlsx Key Reading: Borer, E.T., Seabloom, E.W., Jones, M.B., Schildhauer, M., 2009. Some Simple Guidelines for Effective Data Management. Bulletin of the Ecological Society of America 90, 205–214. White, E. P., E. Baldridge, Z. T. Brym, K. J. Locey, D. J. McGlinn, and S. R. Supp. 2013. Nine simple ways to make it easier to (re) use your data. PeerJ PrePrints. Notes and Instructions for Instructors: Background: Plankton are microscopic organisms that form the base of many aquatic food webs – fueling the growth of fish and other larger organisms. It’s common to sample them using a net or another container that can be controlled to collect water just from certain depths; so you can see how plankton collected at the surface (0 meters) might be different from plankton at another depth (e.g. 10 meters below the surface). (For more information: http://en.wikipedia.org/wiki/Phytoplankton and http://en.wikipedia.org/wiki/Zooplankton.) They are identified and counted under a microscope, and usually their numbers are reported as individuals per liter or milliliter. Frequently, aquatic scientists collect plankton samples during both day (e.g. noon) and night (e.g. 2 am) because plankton change their distributions from day
Transcript of Hands-on Activity 7: Metadata - GitHub Pages...This is some (fictional) information about the...
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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Hands-onActivity7:MetadataAssociatedDataONELecture:Lesson7:MetadataObjectives:Studentsconsiderthelevelofdetailthatisnecessaryformetadatatoadequatelydescribedatasets,andworkwithametadatarecord.Outcomes:(1)Studentscanexplainwhydetailedmetadataarevaluable.(2)Studentscanprovidesuggestionsforimprovingmetadatadescriptions.TimeNeeded:45minutesinclass.URLs:Morpho(https://knb.ecoinformatics.org/#tools/morpho),DataUp(http://dataup.cdlib.org/)AdditionalFilesNeeded:xlsx,zoop-temp-main.xlsx;zoop-temp.xlsxKeyReading:Borer,E.T.,Seabloom,E.W.,Jones,M.B.,Schildhauer,M.,2009.SomeSimpleGuidelinesforEffectiveDataManagement.BulletinoftheEcologicalSocietyofAmerica90,205–214.White,E.P.,E.Baldridge,Z.T.Brym,K.J.Locey,D.J.McGlinn,andS.R.Supp.2013.Ninesimplewaystomakeiteasierto(re)useyourdata.PeerJPrePrints.
NotesandInstructionsforInstructors:
Background:Planktonaremicroscopicorganismsthatformthebaseofmanyaquaticfoodwebs–fuelingthegrowthoffishandotherlargerorganisms.It’scommontosamplethemusinganetoranothercontainerthatcanbecontrolledtocollectwaterjustfromcertaindepths;soyoucanseehowplanktoncollectedatthesurface(0meters)mightbedifferentfromplanktonatanotherdepth(e.g.10metersbelowthesurface).(Formoreinformation:http://en.wikipedia.org/wiki/Phytoplanktonandhttp://en.wikipedia.org/wiki/Zooplankton.)Theyareidentifiedandcountedunderamicroscope,andusuallytheirnumbersarereportedasindividualsperliterormilliliter.Frequently,aquaticscientistscollectplanktonsamplesduring
bothday(e.g.noon)andnight(e.g.2am)becauseplanktonchangetheirdistributionsfromday
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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tonight,andnotallspeciesaltertheirdistributionsinthesameway.(Formoreinformation,search“dielverticalmigration”ontheweb.)Youshouldhave3(fictional)datafiles:pond2010.xlsx,zoop-temp-main.xlsx;zoop-temp.xlsx.These3fileswereallintendedtobepartofthesamestudy–theinvestigatorswantedtoexaminetheday-nightdistributionof2speciesofzooplanktonacrossmultipleyears.Thetypeofzooplanktontheystudiediscalledrotifersgenerally,andspecificallythegenusConochilus,inwhichgroupsofindividualrotiferssticktogetherincolonies(seehttp://eol.org/pages/43393/overview).Theinvestigatorsplantorepeatthisstudyforseveralmoreyears.Thefileshavesomeproblemsinhowtheyareorganized,whichyouhavealreadydiscussedinapreviousexercise.Nowlet’sthinkaboutwritingsomegoodmetadatathatdescribesthedataset.NotethatActivities1-4refertothegrayareasinthemetadatarecord,whichisfoundlaterinthisdocument.
Activity1Asindividualsorinsmallgroups,lookthroughthefilesandlocatealltheinformationthatdescribesthesedata–themetadata.Someofthisinformationisfoundinthishandout,andsomeofitiswithinthe3datasheetsprovided.Describewhereyoufoundtheinformationthatisneededtopopulatethemetadatarecord.Exampleanswer:
Lookatthecolumnheadersinallthesheets,abrieftableonzoop+temp.xlsx,andasecondworksheetonzoop+temp-main.xlsx.Sometraineesmayalsosuggestthatinformationisonlineorelsewhere–e.g.thegeographicalcoordinatesmaybeusedtolocatelakenames,andinformationabouttheorganismsmaybepublished.
Activity2Nowlet’sfocusonametadatadescriptionjustforpond2010.xlsx.Lookatthetablecontainedinthefile.Writeanappropriatetitleforthisdataset.Exampleanswer:
Therearemanygoodanswersherebutwearelookingforverydescriptivetitles,andconsiderthatkeywordscanbeusedtocomplementthetitlessothattheydon’tgettoolong!Here’sonesuggestion:SummerpopulationdensityandcolonysizeofConochilushippocrepisandConochilusunicornisatmultipleponddepthsinLittlevickPondNaturalReserve,Surrey,UKin2010
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Activity3“TimePeriodofContent”representsthetimeperiodthedatawascollected.Whatdateswouldyouenter?Exampleanswer:
Looktothecolumnsfordates.5June2010–18June2010isthetimeperiodcoveredbypond2010.xlsx.InthemetadatarecordthedateswouldberepresentedasYYYYMMDD:20100605and20100618.
Activity4Whatwouldbesomeappropriatethemekeywordsforthisdataset?Wherecanyoufindhelpfordevelopingkeywords?Exampleanswer:
Again,therearemanygoodanswershere.Youmayfindthatsomeofthesametermsappearinboththetitleandkeywordssection.Wordsmightbetaxonomiclike:rotifers,zooplankton,plankton.Theymaydescribetheprocessthattheresearchersarestudyingsuchas:dielverticalmigration.TaxonomicreferencesmayincludeCowardinWetlandClassificationSystemandotherdisciplinespecifictaxonomies.PlaceKeywordthesauricouldincludeGeographicNamesIndexService(GNIS).Discussrelevanttaxonomieswithparticipants.
Activity5Takealookatthemetadatarecordinthisexercise.Notethatthereareavarietyofdomaintypes,andsomearenotedas“unrepresentable.”Whatthatmightmean?Exampleanswer:
Attributessuchastemperature,diameter,anddensityarelistedas“unrepresentable”insteadoflistingarangeofvalues(ie,10-30cm)becausethereisnoabsolutemaxandminvaluefortheattributenotedanywhere.A“percent”attributeisagoodexampleofarangedomainbecausethevaluesmustbegreaterthanorequalto0andlessthanorequalto100.
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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Pond2010MetadataThisissome(fictional)informationaboutthe(fictional)datasetcalledpond2010.xlsx.Thedatasetcanbeusedtofillinmetadatafieldsinaformalrecord,suchastheonebelow,butnotethattheremayalsobeadditionalimportantmetadatawithinthepond2010fileanditsrelatedfiles,zoop-temp-main.xlsxandzoop-temp.xlsx.TitleoftheDataset
Originator/DatasetAuthor AnnaSassinDanD.Lyons
Abstract Thisdatasetisoneofacollectionoffourpopulationsurveydatasetsdocumentingcolonygrowth,reproduction,andsurvivaloftworotiferspecies(ConochilusunicornisandConochilushippocrepis)atfourtimeperiodsoftheyear.Thisdatasetdescribespopulationdataforthesummerseason.SamplesofbothspeciesweretakenatLittlevickpond,Surrey,UK.Measurementstakenincludedepth,temperature,colonydensityandcolonydiameter.
Purpose DatawerecollectedtoevaluatehowtemperatureanddepthaffectthesurvivalofrotifercoloniesinpondswithintheUK.
Publication Publisher:InternationalRotiferRecoveryScienceCenterPlace:Surrey,UKPublication_Date:12/08/2012SeriesName:FourSeasonRotiferSurveyNameofIssue:SummerSurvey
Larger_Work_Citation Originator:Sassin,AnnaandLyons,Dan.D.Publication_Date:12/08/2012Title:Relationshipsbetweenpopulationandtemperature:TrackingrotifersoverthecourseoffourseasonsintheUnitedKingdom.Publisher:RotiferConservationPlace:UKVolume;Issue;Pages:4(2):325-340
TimePeriodofContent BeginDate:EndDate:
CurrentnessReference GroundCondition
Progress/status:
Complete
Maintenance_and_Update_Frequency
Noneplanned
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Geographiccoverage LittlevickPondNaturalReserve,Surrey,UK.Bounding_Coordinates:
West_Bounding_Coordinate:-0.92456818028327East_Bounding_Coordinate:0.371818538415North_Bounding_Coordinate:51.511581803063South_Bounding_Coordinate:50.808817656094
Keywords(theme)
Keywords(place)
SurreyUKInternationalLittlevickPondNaturalReserve
Keywords(temporal) summer,JuneDataAccess_Constraints Nolegalorpolicyrestrictionforaccessingthisdataset.DataUse_Constraints:
Mustproperlyciteoriginatorifusedinpublications,reports,presentations,etc.PleasecitedatasetaccordingtoDataCite.orgstandards
Contact_Person_Primary:
Contact_Person:TadPohl(Datasteward)Contact_Organization:InternationalRotiferRecoveryScienceCenterAddress:5638IndependenceWayCity:GuildfordState_or_Province:Surrey,UKContact_Telephone:+44(0)888-8888
Data_Set_Credit FundingwasprovidedbyInternationalRotiferFoundationAnalytical_Tools SAS,R,MatLabData_Quality_Information Attribute_Accuracy_Report
Temperatureinstrumentwastestedandcalibratedforaccuracybeforeeachsampling.DensityandcolonycountswereconductedaccordingtotheStandardPlateCountprocedure.Countswereconductedbytwodatacounters.Eachtechnicianscountwasverifiedbythesecondtechnician.Countingaccuracywasfoundtobe95%accurate.
Completeness_Report Thedatasetisgenerallycompletealthoughthetemperatureforonesampledepthcouldnotberecordedduetoinstrumentmalfunction.Colonyanddensitycountsarealsomostlycompleteexceptfortwoinstanceswherethedataismissingandisthereforeunknown.Statisticalsummary(boxplot)ofthedatawasperformedandnooutstandingoutliersorpotentiallyerroneousvalueswerefound.
Positional_Accuracy: PositionalAccuracywasnotassessedProcess_Step: Datawascollectedby2peoplethefirstweekandbythesame2
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Process_Description:
peoplethefollowingweek.Watersamplesandtemperatureweretakenatfivedifferentdepths.Inordertoaccountforvariabilityinsamplemeasurements,6watersamplesweretakenateachdepth.These6sampleswerelaterrandomlydividedintotwoevengroupsofthree.Thetwogroupswererandomlyassignedarotiferspeciesnamewherebydatacounterswouldperformthedensityandcolonycountsfortheparticularspecies.
EntityandAttributeInformation
Detailed_DescriptionEntity_Type
Entity_Type_Label:pond2010.xlsxEntity_Type_Definition:Rotiferpopulationsurveyatvariousdepthsandtemperature
Attribute
Attribute_Label:zAttribute_Definition:DepthincentimetersfromthesurfaceAttribute_Domain_Values:Enumerated_Domain:Enumerated_Domain_Value:0.5Enumerated_Domain_Value_Definition:0.5cmbelowsurfaceEnumerated_Domain_Value:5Enumerated_Domain_Value_Definition:5cmbelowsurfaceEnumerated_Domain_Value:10Enumerated_Domain_Value_Definition:10cmbelowsurfaceEnumerated_Domain_Value:25Enumerated_Domain_Value_Definition:25cmbelowsurfaceEnumerated_Domain_Value:50Enumerated_Domain_Value_Definition:50cmbelowsurface
Attribute
Attribute_Label:TemperatureAttribute_Definition:TemperatureofwaterinCelsiusAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:DensityAttribute_Definition:NumberofindividualspercolonyAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:ColonyDiameterAttribute_Definition:LengthoflongestcolonydiameterinmillimetersAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:SpeciesAttribute_Definition:RotiferspeciesAttribute_Domain_Values:Enumerated_Domain_Value:cuni
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Enumerated_Domain_Value_Definition:ConochilusunicornisEnumerated_Domain_Value:chippoEnumerated_Domain_Value_Definition:Conochilushippocrepis
DistributionInformation DistributorContact_InformationContact_Organization_Primary
Contact_Organization:RotiferNetworkforBiocomplexity(RNB)Contact_Person:MetadataCoordinatorAddress:6534BiodataWayCity:NovelJerseyState_or_Province:NewJerseyPostal_Code:97564Contact_Voice_Telephone:555-555-1034Contact_Email:[email protected]
Distribution_Liability
TheRotiferNetworkforBiocomplexity(RNB)shallnotbeheldliableforimproperorincorrectuseofthedatadescribedand/orcontainedherein.Itistheresponsibilityofthedatausertousethedataappropriatelyandconsistentwithinthelimitationsofthedata.
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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StudentInstructions:
Background:Planktonaremicroscopicorganismsthatformthebaseofmanyaquaticfoodwebs–fuelingthegrowthoffishandotherlargerorganisms.It’scommontosamplethemusinganetoranothercontainerthatcanbecontrolledtocollectwaterjustfromcertaindepths;soyoucanseehowplanktoncollectedatthesurface(0meters)mightbedifferentfromplanktonatanotherdepth(e.g.10metersbelowthesurface).
(Formoreinformation:
http://en.wikipedia.org/wiki/Phytoplanktonand
http://en.wikipedia.org/wiki/Zooplankton.)
Theyareidentifiedandcountedunderamicroscope,andusuallytheirnumbersarereportedasindividualsperliterormilliliter.
Frequently,aquaticscientistscollectplanktonsamplesduringbothday(e.g.noon)andnight(e.g.2am)becauseplankton
changetheirdistributionsfromdaytonight,andnotallspeciesaltertheirdistributionsinthesameway.(Formoreinformation,search“dielverticalmigration”ontheweb.)
Youshouldhave3(fictional)datafiles:pond2010.xlsx,zoop-temp-main.xlsx;zoop-temp.xlsx.
These3fileswereallintendedtobepartofthesamestudy–theinvestigatorswantedtoexaminetheday-nightdistributionof2speciesofzooplanktonacrossmultipleyears.Thetypeofzooplanktontheystudiediscalledrotifersgenerally,andspecificallythegenusConochilus,inwhichgroupsofindividualrotiferssticktogetherincolonies(seehttp://eol.org/pages/43393/overview).Theinvestigatorsplantorepeatthisstudyforseveralmoreyears.
Thefileshavesomeproblemsinhowtheyareorganized,whichyouhavealreadydiscussedinapreviousexercise.Nowlet’sthinkaboutwritingsomegoodmetadatathatdescribesthedataset.NotethatActivities1-4refertothegrayareasinthemetadatarecord,whichisfoundlateroninthisdocument.
Activity1Asindividualsorinsmallgroups,lookthroughthefilesandlocatealltheinformationthatdescribesthesedata–themetadata.Someofthisinformationisfoundinthishandout,andsomeofitiswithinthe3datasheetsprovided.Describewhereyoufoundtheinformationthatisneededtopopulatethemetadatarecord.
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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Activity2Nowlet’sfocusonametadatadescriptionjustforpond2010.xlsx.Lookatthetablecontainedinthefile.Writeanappropriatetitleforthisdataset.
Activity3“TimePeriodofContent”representsthetimeperiodthedatawascollected.Whatdateswouldyouenter?
Activity4Whatwouldbesomeappropriatethemekeywordsforthisdataset?Wherecanyoufindhelpfordevelopingkeywords?
Activity5Takealookatthemetadatarecordinthisexercise.Notethatthereareavarietyofdomaintypes,andsomearenotedas“unrepresentable.”Whatthatmightmean?
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
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Pond2010MetadataThisissome(fictional)informationaboutthe(fictional)datasetcalledpond2010.xlsx.Thedatasetcanbeusedtofillinmetadatafieldsinaformalrecord,suchastheonebelow,butnotethattheremayalsobeadditionalimportantmetadatawithinthepond2010fileanditsrelatedfiles,zoop-temp-main.xlsxandzoop-temp.xlsx.TitleoftheDataset
Originator/DatasetAuthor AnnaSassinDanD.Lyons
Abstract Thisdatasetisoneofacollectionoffourpopulationsurveydatasetsdocumentingcolonygrowth,reproduction,andsurvivaloftworotiferspecies(ConochilusunicornisandConochilushippocrepis)atfourtimeperiodsoftheyear.Thisdatasetdescribespopulationdataforthesummerseason.SamplesofbothspeciesweretakenatLittlevickpond,Surrey,UK.Measurementstakenincludedepth,temperature,colonydensityandcolonydiameter.
Purpose DatawerecollectedtoevaluatehowtemperatureanddepthaffectthesurvivalofrotifercoloniesinpondswithintheUK.
Publication Publisher:InternationalRotiferRecoveryScienceCenterPlace:Surrey,UKPublication_Date:12/08/2012SeriesName:FourSeasonRotiferSurveyNameofIssue:SummerSurvey
Larger_Work_Citation Originator:Sassin,AnnaandLyons,Dan.D.Publication_Date:12/08/2012Title:Relationshipsbetweenpopulationandtemperature:TrackingrotifersoverthecourseoffourseasonsintheUnitedKingdom.Publisher:RotiferConservationPlace:UKVolume;Issue;Pages:4(2):325-340
TimePeriodofContent BeginDate:EndDate:
CurrentnessReference GroundCondition
Progress/status:
Complete
Maintenance_and_Update_Frequency
Noneplanned
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
11
Geographiccoverage LittlevickPondNaturalReserve,Surrey,UK.Bounding_Coordinates:
West_Bounding_Coordinate:-0.92456818028327East_Bounding_Coordinate:0.371818538415North_Bounding_Coordinate:51.511581803063South_Bounding_Coordinate:50.808817656094
Keywords(theme)
Keywords(place)
SurreyUKInternationalLittlevickPondNaturalReserve
Keywords(temporal) summer,JuneDataAccess_Constraints Nolegalorpolicyrestrictionforaccessingthisdataset.DataUse_Constraints:
Mustproperlyciteoriginatorifusedinpublications,reports,presentations,etc.PleasecitedatasetaccordingtoDataCite.orgstandards
Contact_Person_Primary:
Contact_Person:TadPohl(Datasteward)Contact_Organization:InternationalRotiferRecoveryScienceCenterAddress:5638IndependenceWayCity:GuildfordState_or_Province:Surrey,UKContact_Telephone:+44(0)888-8888
Data_Set_Credit FundingwasprovidedbyInternationalRotiferFoundationAnalytical_Tools SAS,R,MatLabData_Quality_Information Attribute_Accuracy_Report
Temperatureinstrumentwastestedandcalibratedforaccuracybeforeeachsampling.DensityandcolonycountswereconductedaccordingtotheStandardPlateCountprocedure.Countswereconductedbytwodatacounters.Eachtechnicianscountwasverifiedbythesecondtechnician.Countingaccuracywasfoundtobe95%accurate.
Completeness_Report Thedatasetisgenerallycompletealthoughthetemperatureforonesampledepthcouldnotberecordedduetoinstrumentmalfunction.Colonyanddensitycountsarealsomostlycompleteexceptfortwoinstanceswherethedataismissingandisthereforeunknown.Statisticalsummary(boxplot)ofthedatawasperformedandnooutstandingoutliersorpotentiallyerroneousvalueswerefound.
Positional_Accuracy: PositionalAccuracywasnotassessedProcess_Step: Datawascollectedby2peoplethefirstweekandbythesame2
Hands-on Exercises for Data Management http://www.dataone.org/education-modules
12
Process_Description:
peoplethefollowingweek.Watersamplesandtemperatureweretakenatfivedifferentdepths.Inordertoaccountforvariabilityinsamplemeasurements,6watersamplesweretakenateachdepth.These6sampleswerelaterrandomlydividedintotwoevengroupsofthree.Thetwogroupswererandomlyassignedarotiferspeciesnamewherebydatacounterswouldperformthedensityandcolonycountsfortheparticularspecies.
EntityandAttributeInformation
Detailed_DescriptionEntity_Type
Entity_Type_Label:pond2010.xlsxEntity_Type_Definition:Rotiferpopulationsurveyatvariousdepthsandtemperature
Attribute
Attribute_Label:zAttribute_Definition:DepthincentimetersfromthesurfaceAttribute_Domain_Values:Enumerated_Domain:Enumerated_Domain_Value:0.5Enumerated_Domain_Value_Definition:0.5cmbelowsurfaceEnumerated_Domain_Value:5Enumerated_Domain_Value_Definition:5cmbelowsurfaceEnumerated_Domain_Value:10Enumerated_Domain_Value_Definition:10cmbelowsurfaceEnumerated_Domain_Value:25Enumerated_Domain_Value_Definition:25cmbelowsurfaceEnumerated_Domain_Value:50Enumerated_Domain_Value_Definition:50cmbelowsurface
Attribute
Attribute_Label:TemperatureAttribute_Definition:TemperatureofwaterinCelsiusAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:DensityAttribute_Definition:NumberofindividualspercolonyAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:ColonyDiameterAttribute_Definition:LengthoflongestcolonydiameterinmillimetersAttribute_Domain_Values:Unrepresentable_Domain
Attribute
Attribute_Label:SpeciesAttribute_Definition:RotiferspeciesAttribute_Domain_Values:Enumerated_Domain_Value:cuni
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Enumerated_Domain_Value_Definition:ConochilusunicornisEnumerated_Domain_Value:chippoEnumerated_Domain_Value_Definition:Conochilushippocrepis
DistributionInformation DistributorContact_InformationContact_Organization_Primary
Contact_Organization:RotiferNetworkforBiocomplexity(RNB)Contact_Person:MetadataCoordinatorAddress:6534BiodataWayCity:NovelJerseyState_or_Province:NewJerseyPostal_Code:97564Contact_Voice_Telephone:555-555-1034Contact_Email:[email protected]
Distribution_Liability
TheRotiferNetworkforBiocomplexity(RNB)shallnotbeheldliableforimproperorincorrectuseofthedatadescribedand/orcontainedherein.Itistheresponsibilityofthedatausertousethedataappropriatelyandconsistentwithinthelimitationsofthedata.
