Chapter 4
Contents
1. Table 2 Two examples to show how to convert longitude latitude data from degrees to decimal Names form the major key for accessing information in primary species databases If the name is wrong then access to the information by users will be difficult if not impossible Table 3 shows what may happen when entering names in a non standard way This is an extreme example but misspellings of names are the most frequent error in taxonomic databases 57 Actinobacillus actimomycetemcomitans Actinobacillus actimycetemcomitans Actinobacillus actinmycetemcomitans Actinobacillus actinomicetemcomitans Actinobacillus actinomy Actinobacillus actinomyce Actinobacillus actinomycemcomitans Actinobacillus actinomyceremcomitans Actinobacillus actinomycetecomitans Actinobacillus actinomycetemcmitans Actinobacillus actinomycetemcomintans Actinobacillus actinomycetemcomitance Actinobacillus actinomycetemcomitans Actinobacillus actinomycetemcomitants Actinobacillus actinomycetemcommitans Actinobacillus actinomycetum Actinobacillus actinomyctemcomitans Actinobacillus actinomyectomcomitans Actinobacillus actinomyetemcomitans Actinobacillus actinonmycetemcomitans Actinobacillus actionomycetemcomitans Actinobacillus actynomicetemcomitans Actinobacill Actinobacillus Actinobacillus CENORACIUS actinomycetemocimitans antinomycetemcomitans actinomycetam Actinobacillus Anon echs actinomyce2. 8 745 767 WAKCHAURE A 2006 An Application for Birdwatchers Final Report see http ashwinimail web officelive com Documents 0_website_GPS_birding_app p df accessed 4 Oct 2009 66 10 Technical References FRANCKI R I B FAUQUET C M KNUDSON D L amp BROWN F 1990 Classification and Nomenclature of Viruses Archives of Virology Suppl 2 1 445 INTERNATIONAL CODE OF BOTANICAL NOMENCLATURE 2000 International Code of Botanical Nomenclature St Louis Code Regnum Vegetabile 138 K nigstein Koeltz Scientific Books see http www bgbm fu berlin de iapt nomenclature code SaintLouis 0001ICSLContents htm accessed 4 Oct 2009 INTERNATIONAL CODE OF ZOOLOGICAL NOMENCLATURE 2000 International code of zoological nomenclature adopted by the International Union of Biological Resources International Commission on Zoological Nomenclature 4th edition London International Trust for Zoological Nomenclature see http www iczn org iczn index jsp accessed 4 Oct 2009 SNEATH P H A Ed 1992 International Code of Nomenclature of Bacteria 1980 Revision Washington International Committee on Systematic Bacteriology ICSB see http Awww ncbi nim nih gov bookshelf br fcgi book icnb accessed 4 Oct 2009 TREHANE P BRICKELL C D BAUM B R HETTERSCHEID W L A LESLIE A C MCNEILL J SPONGBERG S A amp VRUGTMAN F 1995 International Code of Nomenclature for Cultivated Plants Winbourne UK Q
3. geographic area BETTER Locke Sacramento River Delta Sacramento Co California names a town within the Delta Names of Roads BAD Highway 9 Alajuela Province Costa Rica without additional GOOD Intersection of Hwy 9 and Rio Cariblanco Cariblanco points of reference town Alajuela Province Costa Rica Localities difficult to For many countries especially Spanish speaking ones there are Georeference oftentimes several cities with the same name in the same province BAD San Marcos Intibuca Province Honduras There are at least five San Marcos in Intibuca Province BETTER San Marcos ca 7 5 km south of Los Chaguites Intibuca Province Honduras Table 1 Some examples for good and bad locality descriptions from Museum of Vertebrate Zoology 2009a Guide for recording localities Museum of Vertebrate Zoology 2009b e Full Locality Name Provide a descriptive locality even if you have geographic coordinates Write the description from specific to general including a specific locality offset s from a reference point and administrative units such as county state and country The locality should be as specific succinct unambiguous complete and accurate as possible leaving no room for uncertainty in interpretation Hint The most specific localities are those described by a a distance and heading along a path from a nearby and well defined intersection or b two cardinal offset distances from a si
4. of use One application is for birdwatchers and it focuses on birding sites near Gainesville Wakchaure 2006 Another application with customized ArcPad forms was developed for an earthworm inventory to be conducted during summer 2004 Dabrowski 2004 This study would measure the impact of European earthworm invasions on vegetation and soil characteristics at two Great Lakes national parks Pictured Rocks National Lakeshore located in the Upper Peninsula of Michigan and Voyageurs National Park located in northern Minnesota Another software for ecological data entry is Pocket eRelev http ereleve codeplex com accessed 4 Dec 2009 designed for naturalists This program is developed in Visual Basic and only available in French For bird 59 watchers an application exists called Pocket Bird Recorder to record sightings in the field with mobile devices http www wildlife co uk accessed 4 Dec 2009 5 1 ATBI M approach one example for an application with customized forms for ArcPad The example discussed in detail for electronic data recording in the field is the application for mobile recording with customized forms for ATBI M sites These forms are for mobile devices with the installed software ArcPad a tool from ESRI Inc The system requirements are a Windows Mobile operating system Microsoft Active Sync 4 5 for desktop synchronization and a Microsoft XML Parser These forms are available at http www atbi eu The basi
5. C Recommendations Document Pointer http www opengeospatial org standards is accessed 4 Oct 2009 9 References BIOCASE 2003 Biological Collection Access Service for Europe see http www biocase org accessed 4 Oct 2009 CHAPMAN A D 2004a Environmental Data Quality b Data Cleaning Tools Appendix to Sistema de Informa o Distribu do para Cole es Biol gicas A Integra o do Species Analyst e SinBiota FAPESP Biota process no 2001 02175 5 March 2003 March 2004 CRIA Campinas Brazil 57 pp see http splink cria org br docs appendix i pdf accessed 30 Sep 2009 CHAPMAN A D 2004b Guidelines on Biological Nomenclature Brazil edition Appendix J to Sistema de Informa o Distribu do para Cole es Biol gicas A Integra o do Species Analyst e SinBiota FAPESP Biota process no 2001 02175 5 March 2003 March 2004 CRIA Campinas Brazil 11 pp see http splink cria org br docs appendix j pdf accessed 30 Sep 2009 CHAPMAN A D 2005a Principles of Data Quality version 1 0 Report for the Global Biodiversity Information Facility Copenhagen CHAPMAN A D 2005b Uses of Primary Species Occurrence Data version 1 0 Report for the Global Biodiversity Information Facility Copenhagen CHAPMAN A D amp WIECZOREK J Eds 2006 Guide to Best Practices for Georeferencing Global Biodiversity Information Facility Copenhagen see www gbif es ficheros Colombia Georeferencing Best Practi
6. Chapter 4 Individual records and the associated data information standards and protocols by Alexander Kroupa European Distributed Institute of Taxonomy EDIT Museum fir Naturkunde Leibniz Institute for Research on Evolution and Biodiversity Invalidenstr 43 10115 Berlin Germany Email alexander kroupa mfn berlin de David Remsen Global Biodiversity Information Facility GBIF Universitetsparken 15 2100 Copenhagen Denmark Email dremsen gbif org 49 Abstract The structure of databases with taxonomic content is very important to ensure a compatibility with other database systems For the exchange of taxonomic information it is necessary to have standards and protocols to permit the presentation e g on a web system like GBIF of species data from different database sources For ATBI M projects a guideline for recording species has been developed with the minimal requirements for a high data quality standard Also standards are used errors may occur along the information management chain from data recording up to data presentation Error sources can be within the geo referenced domain as well as in the taxonomic domain Therefore software for automated geo referencing and recording of date and time in standardized formats for mobile phones with GPS up to water resistant PDAs have to be developed The gain of using those field tools is improving data quality and simplifying the data recording for a cost effective process to obtai
7. TM Universal Transverse Mercator WDPA World database on protected areas WFS web feature services WMS web mapping features 8 Key links Access to Biological Collection Data ABCD http wiki tdwg org twiki bin view ABCD accessed 4 Oct 2009 TDWG Wiki for ABCD http www bgbm org tdwg codata schema ABCD_2 06 HTML ABCD_2 06 html XSLT Schema accessed 4 Oct 2009 DIVA GIS http www diva gis org accessed 4 Oct 2009 Environmental Resources Information Network ERIN http www deh gov au erin index html accessed 4 Oct 2009 GEOLocate University of Tulane http www museum tulane edu geolocate accessed 4 Oct 2009 Mammal Networked Information System MaNIS http manisnet org accessed 4 Oct 2009 http manisnet org Documents html MaNIS Documents accessed 4 Oct 2009 http manisnet org GeorefGuide html Georereferencing Guidelines accessed 4 Oct 2009 Museum of Vertebrate Zoology Informatics MVZ University of California Berkeley http mvz berkeley edu Informatics html accessed 4 Oct 2009 64 http mvz berkeley edu Locality Field Recording Notebooks html Guide for Recording Localities in the Field accessed 4 Oct 2009 http mvz berkeley edu Locality Field Recording examples html Examples of Good and Bad Localities accessed 4 Oct 2009 http mvz berkeley edu Locality Field Recording important html Why it is Important to Take Good Locality Data accessed 4 Oct 2009 OG
8. ain consistency when a controlled list is not available If it is not possible to use authority lists a recommendation is than to process the collected information as quickly as possible after the fieldwork The structure of the database has to be clear unambiguous and consistent The taxon information should be atomized so that it is always clear that one field includes just the genus or the species name and is not mixed to have just one field with the genus and the species name together One should always atomize the taxonomic information into separate Genus Species infraspecific Rank Infraspecies Author fields etc wherever possible Guide for recording the minimum taxonomy for species level taxa e Genus name The genus name is essential Hint Do not use any abbreviation e Species name The species name is essential Hint Do not use any abbreviation e Authors of a species name The author s name should be included to ensure a unique mapping in case of homonyms e Determinator The name of the person s who is responsible for the determination of the collection observation Hint Do not use any abbreviation write the full name 55 e Taxon Source A reference to a taxonomic guide or treatment that forms the basis for the identification Species are often lumped with or split from other taxa over the course of revisions Ambiguity is reduced by providing a reference to particular taxonomic view that provides a specific sense o
9. aps which are a longer period in the field it is necessary to have a date for the end of the research Hint Use the end date also when the fieldwork takes only a couple of hours e Collector s Provide the name of each collector and when relevant the name of the expedition or research vessel i e boat Hint Do not use abbreviations write the full name including second names or attributes like senior junior to identify the collectors uniquely and avoid ambiguity of homonyms or families of collectors over several generations 2 3 Taxonomy what Names whether they are scientific binomials or common names provide the first point of entry to most species and species occurrence databases The correct spelling of a scientific name is generally governed by one of the various Codes of Nomenclature see list under Technical References Errors can still occur however through typing errors ambiguities in the Nomenclatural Code etc The easiest method to ensure such errors are kept to a minimum is to use an Authority File during recording of data Chapman 2004a An authority file is a pre composed list of verified species names Current lists of species names may be found at a number of places and some of these are listed in Chapman 2004b e g Species2000 FaunaEuropaea 4D4Life Also the re use of entered terms via internal controlled lists in an application that provides pull down lists of previously entered terms can help maint
10. ays be a need for the application of validation and annotation services as post publication processes as well 58 5 New technologies for data recording It is necessary to develop tools for recording spatial and taxonomic data in the field for a number of reasons In particular it is cost effective to avoid mistakes right at the beginning of the recording chain Fig 2 Each error which is not made saves a lot of time Errors may be avoided by using authority lists e g for countries habitat types or species groups that can be determined to a great part in the field Automated geo referencing and recording of date and time in standardized formats will also avoid typing errors by rewriting the data from paper to a database The gain of using field tools is improving data quality and simplifying the data recording AN Data editing Data Or Presentation World Wide Web A E g cleaning and Release Gollector SBS EST A m Ce O Qeeteperstesnedionicees of error correction increases Fig 2 Information Management Chain showing that the cost of error correction increases as one progresses along the chain modified from Chapman 2005a The developed software has to be usable for mobile phones with GPS up to water resistant PDAs e g Magellan Mobile Mapper Trimble Juno Nomad For ArcPad software from ESRI Inc some applications are already developed for recording data in the field for different types
11. bly more than 100 000 scientific biological records observations collected specimens are recorded personal estimation Many of these data are still not digitally recorded and the majority of these data are not recorded using standard protocols or proper referencing The goal is that all recorded datasets should be properly referenced and that all individual field records must be accurately geo referenced with an exact date or interval Therefore more and more electronic tools and software have to be used to facilitate the recording of species data sets and to minimize the amount of errors This chapter provides a review of the important data structure elements of primary occurrence data with the inclusion of best practices and recommendations in their use 2 Data structure Species occurrence data is used to include specimen label data attached to specimens or lots housed in museums and herbaria or in Universities NGOs Amateurs associations etc observational data e g birdwatchers and environmental survey data Chapman 2005a The term has occasionally been used interchangeably with the term primary species data In general we speak about geo referenced data e g records with geographic references that tie them to a particular place in space whether with a geo referenced coordinate e g latitude and longitude UTM or not textual description of a locality altitude depth Normally the data are referred to as
12. ccessed 18 Sep 2009 PEABODY MUSEUM n dat BioGeoMancer see http www biogeomancer org accessed 4 Oct 2009 R VEILLON A 2009 The GBIF Integrated Publishing Toolkit User Manual version 1 0 Global Biodiversity Information Facility Copenhagen 37 pp see http gbif providertoolkit googlecode com files GBIF IPT User Manual 1 0 pdf accessed 3 Dec 2009 Rios N E amp BART H L JR n dat GEOLocate Georeferencing Software User s Manual Belle Chasse LA USA Tulane Museum of Natural History see http www museum tulane edu geolocate support manual ver2 O pdf accessed 4 Oct 2009 SHATTUCK S O 1997 eGaz The Electronic Gazetteer ANIC News 11 9 SOURCEFORGE 2004 Distributed Generic Information Retrieval DiGIR see http digir sourceforge net accessed 4 Oct 2009 TDWG 2004 ABCD Schema Task Group on Access to Biological Collection Data see _http bgbm3 bgbm fu berlin de TDWG CODATA default htm accessed 4 Oct 2009 VIEGLAIS D 2003 The Darwin Core Revision 1 5 Lawrence KA University of Kansas Natural History Museum and Biodiversity Research Center WIECZOREK J 2001 MaNIS HerpNel ORNIS Georeferencing Guidelines see http manisnet org GeorefGuide html accessed 30 Sept 2009 WIECZOREK J GUO Q amp HIJMANS R J 2004 The point radius method for georeferencing locality descriptions and calculating associated uncertainty Int J Geographical Information Science 18
13. ces pdf accessed 24 Jun 2009 CRIA 2004 GeoLoc CRIA Campinas Centro de Refer ncia em Informa o Ambiental see http splink cria org br tools accessed 4 Oct 2009 DABROWSKI J 2004 Experiences developing a custom ArcPad solution for an Earthworm Inventory see http science nature nps gov im units mwr documents APExperiences pdf accessed 4 Oct 2009 DALCIN E C 2005 Data Quality Concepts and Techniques Applied to Taxonomic Databases University of Southampton Faculty of Medicine Health and Life Sciences 266 pp EDIT 2009 Data recording guidelines for ATBI M pilot sites see http www atbi eu wp files common Excel sheet for locality and event entry xls accessed 30 Sep 2009 65 HELLERSTEIN J M 2008 Quantitative data cleaning for large databases White paper United Nations Economic Commission for Europe 42 pp see http db cs berkeley edu jmh papers cleaning unece pdf accessed 21 Sep 2009 MALETIC J l amp MARCUS A 2000 Data Cleansing Beyond Integrity Analysis Division of Computer Science Department of Mathematical Sciences The University of Memphis Memphis 10 pp MUSEUM OF VERTEBRATE ZOOLOGY 2009a Examples of Good and Bad Localities see http mvz berkeley edu Locality Field Recording examples html accessed 18 Sep 2009 MUSEUM OF VERTEBRATE ZOOLOGY 2009b MVZ Guide for Recording Localities in Field Notes see http mvz berkeley edu FieldLocalities doc a
14. heterogeneous sources using common standards and protocols GBIF developed the Integrated Publishing Toolkit The GBIF IPT is an Open source Java based web application It embeds its own database is easily customisable and is multilingual The data registered in a GBIF IPT instance is connected to the GBIF distributed network and made available for public consultation and use via established data access formats and protocols that include TAPIR and Open Geospatial Consortium OGC web mapping and web feature services WMS and WFS R veillon 2009 Simple transformations of the DarwinCore Archive file would also support the creation of Keyhole Markup Language KML files for use within Google earth fieldwork Facilitated data entry Fig 9 Data flow from the field recording with GPS tools to different internet presentations 6 Acknowledgements We wish to thank A D Chapman and J Wieczorek who due to their publications created a profound basis for this chapter 7 Acronyms ABCD Access to Biological Collections Data ATBI M All Taxa Biodiversity Inventory Monitoring 63 BioCASE Biological Collection Access Service DiGIR Distributed Generic Information Retrieval GBIF Global Biodiversity Information Facility GPS Global Positioning System IPT Integrated Publishing Toolkit KML Keyhole Markup Language OGC Open Geospatial Consortium TAPIR TDWG Access Protocol for Information Retrieval TDWG Taxonomic Databases Working Group U
15. itude level But it is also possible to write values into these fields if other tools for measuring the altitude are used Everybody has to bear in mind that the accuracy of the altitude measurement with GPS tools is very low It is about 10 times lower than the accuracy for longitude or latitude The used coordinate system can be selected with a list box 5 1 2 Event forms For each locality more than one event can be created see 2 2 Therefore a form exists to list all existing events for one locality Fig 5 The events are listed chronological with the start date of the events Each event can be edited or deleted deleting will delete also the attached species list Geo Event List 4 gt Event EventCode 07 ETE 200807 1 22 8 2009 15 40 Start set Start 4 9 2009 14 26 4 9 2009 14 26 set Star End setEnd 4 9 2009 15 47 Collector ja Kroupa Col Method by hand Event sunny day 32 C Remarks new edit delete save Set up species list BO Ve Fig 5 List of all events belonging to one Fig 6 Editform for one event The value Locality ordered in chronological sequence of the start time will be set automatically The values for the start time and end time can be set also by pressing the button set Start respectively set End 61 The detail data for each event consists of one EventCode and of the start and the end date time of this event Fig 6 The start date will be created au
16. n high quality taxonomic information Key words taxonomic database standards data quality field tools ATBI M 50 1 Introduction Taxonomic databases databases that store information about biological entities species and other taxa have been developed to address curatorial management requirements taxonomic and scientific needs and more recently for presentation of species data distribution maps pictures biology etc to a wider public Dalcin 2005 These databases have the taxon as the principal entity represented by its main identification the taxon name Taxonomic databases often have a focus on terminal taxa species and infraspecies levels which consist of a genus and species name and when applicable additional infra species names Data or Information is tied to the taxon and typically falls into two levels of organisation either elements that relate to the taxon as a whole or elements that relate to specific instance of a taxon The latter class of information is known as species occurrence or primary occurrence data Primary occurrence data include data elements that describe a taxon occurrence such as a date a species may have been collected or a location where it was observed General species data on the other hand describe properties ascribe to the entire taxon such as a general morphological description or a range map In this chapter we will focus on databases for primary occurrence data Every day proba
17. ngle nearby feature of small extent 53 e Altitude Elevation Supplement the locality description with elevation information Hint A barometric altimeter when properly calibrated is much more reliable than a GPS for obtaining accurate elevations e Coordinates Whenever practical provide the coordinates of the location where collecting actually occurred see Radius below If reading coordinates from a map use the same coordinate system as the map Hint Decimal degrees coordinates are preferred when reading coordinates from a GPS and if possible provide lat long data e Geographic Datum The datum is an essential part of a coordinate description it provides the frame of the reference When using both maps and GPS in the field set the GPS datum to be the same as the map datum so that your GPS coordinates will match those on the map Hint Always record the datum with the coordinates e GPS Accuracy Record the accuracy as reported by the GPS whenever you take coordinates Hint Most GPS devices do not record accuracy with the waypoint data but provide it in the interface showing current satellite conditions e Radius Extent The extent is a measure of the size of the area within which collecting or observations occurred for a given locality the distance from the point described by the locality and coordinates to the furthest point where collecting or observations occurred in that locality Hint A 1 km linear trap line fo
18. perties as altitude or spatial data the increasing proliferation of sensor technology has led to exact measurements Nevertheless data errors are still quite common selection and placement of sensors often affects data quality and by transferring data to the database errors may occur Converting coordinates from one system to another may cause errors and converting longitude latitude data from degrees to decimal may often result in a wrong calculation Table 2 Distillation errors In many settings raw data are preprocessed and summarized before they are entered into a database This data distillation is done for a variety of reasons and has the potential to produce errors in distilled data or in the way that the distillation technique interacts with the final analysis Data integration errors Any procedure that integrates data from multiple sources can lead to errors To minimize integration errors standards are necessary to ensure that fields contain the same entity type That e g a species field contains only the species epithet and not genus and epithet together latitude longitude formula calculation decimal result 44 16 12 01 7 23 degrees minutes 44 16 60 12 01 44 27000278 48 50 60 seconds 3600 7 7 39680556 3600 23 60 48 50 3600 44 15 368 7 22 86 degrees minutes 44 15 368 60 7 44 2728 7 381 60 22 86 60
19. point based although line transect data from environmental surveys collections e g along a river polygon observations from within a defined area such as a national park and grid data observations or survey records from a regular grid are also included Usually the data are also tied to a taxonomic name but unidentified collections 51 may also be included by referencing to a higher taxon group e g Unidentified Aves For sampling species data it is necessary to record not only where a geospatial location the species were found but also when date and time what taxonomy how collecting method and who collected observed the specimen Each locality where may have different events Fig 1 which means that sampling at more than one date or with different sampling methods have been carried out Each event in turn may have its own species list or even more than one list if different researchers built their own lists for the same event Taxonomy Fig 1 Context of Locality Event and Taxonomy by recorded species data 2 1 Localities where Good locality descriptions lead to more accurate geo references with smaller uncertainty values and provide users with much more accurate and high quality data When recording data in the field whether from a map or when using a GPS it is important to record locality information as well as the geo references so that later validation can take place if neces
20. r definition of the taxon as used by the identifier e Number The number of the individuals observed or collected Hint Use only numbers and no text not 2 3 3ff some abundant etc e Deposit For further studies the deposit of collected material should be recorded Hint Abbreviations have to be well defined better do without abbreviations Add the town of the museum especially if it is not a well known museum e Family and other higher parent taxa The family or higher taxon that includes the referenced species This information may be useful for providing taxonomic context in later references to the record 3 Standards Since more and more taxonomic databases are appearing both institutional and individual concern about sharing data is rising At this moment the need to establish data standards and communication protocols is obvious in order to make data sharing between different databases possible Dalcin 2005 A number of recent collaborations within the museum community have resulted in establishing data standards Examples include the Darwin Core Schema Vieglais 2003 along with the DiGIR protocol SourceForge 2004 and the combined BioCASE protocol BioCASE 2003 and ABCD schema TDWG 2004 that are more fitted for interchange of primary species information The Biodiversity Information Standards TDWG and others developed a new protocol TAPIR http ww3 bgbm org tapir that supports multiple data formatting standa
21. r which the coordinates refer to the centre has an extent of 0 5 km e References Record the sources of all measurements Minimally include map name GPS model and the source for elevation data For including geo referenced records or observations into a database the point radius method is commonly used Wieczorek et al 2004 This method describes a locality as a coordinate pair important always include the geographic datum and a distance from that point that is a circle the combination of which encompasses the full locality description and its associated uncertainties GPS accuracy The key advantage of this method is that the uncertainties can be readily combined into one attribute With modern GPS devices the uncertainties are usually less than 10 m To include historical data from natural history collections this method is also useable when localities have typically been recorded as textual descriptions without geographic coordinates The calculation of the radius takes into account aspects of the precision and specificity of the locality description as well as the map scale datum precision and accuracy of the sources used to determine coordinates 2 2 Events when Guide for recording events e Start Date The date of the collection or observation should at least be recorded and if available the time as well Hint use a date format e g DD MM YYYY and a time format hh mm ss 54 e End Date For intervals e g tr
22. rds that is intended to provide a single solution for publishing data to the GBIF network TAPIR can be implemented in multiple degrees of complexity and capacity lite medium full but importantly still require advanced technical skills to install and maintain The newest and ratified Darwin Core terms provides a unified approach to publishing both species level and species occurrence level data using a common standard This DarwinCore Archive format is being championed by GBIF and while it is a supported output of the Integrated Publishing Toolkit provides a simple enough data publication solution that it can be output as a direct database export by many data managers For recording geo referenced species data a guideline with the most important fields for species occurrence data has been developed within the EDIT project EDIT 2009 This structure has been developed especially for recording data in the ATBI M sites and is used by everyone sampling for ATBI purposes It may also be used as a base for creating own databases 56 4 4 1 Errors Sources of error in data Hellerstein 2008 Data entry errors It remains common in many settings for data entry to be done by humans by keying in data from written or printed sources e g after fieldwork In these settings data is often corrupted at entry time by typographic errors or misunderstanding of the data source see 2 3 Measurement errors In the measurement of physical pro
23. s of this application is the programming of the Earthworm project with the customized ArcPad forms for selecting species named Species Picker Dabrowski 2004 5 1 1 Locality forms For recording locality information two customized forms exist On the first form Fig 3 a code and a name for the locality is arbitrary The country can be selected from a list box and specifications to the macrohabitat and remarks can be made see 2 1 x Locality Geo E4 Locality code i Locality name Juniperus Country Germany v Macrohabitat Juniper open scrub habitat on exposed rock face Remarks j S N x Locality Geo a E gt Latitude Es Longitude Es Accuracy m mooo Radius m o EE o om Altitude m set Min set Max Coord Sys was 1984 E 4 Fig 3 Editform for Locality data Fig 4 Editform for the geo referenced data Locality code has to be unique The values of latitude longitude and altitude will be set automatically if GPS is switched on The values for the altitude range can be set also by pressing the button set Min respectively set Max 60 On the second form Fig 4 information to the geo referencing of the locality can be filled in Latitude longitude accuracy and the minimum altitude are filled in automatically The minimum and maximum altitude may be set with the two buttons set Min and set Max in the case the research area is not on one alt
24. sary Chapman amp Wieczorek 2006 One purpose behind a specific locality description is to allow the validation of coordinates in which errors are otherwise difficult to detect The extent to which validation can occur depends on how well the locality description and its spatial counterpart describe the same place The highest quality locality description is one with as few sources of uncertainty as possible By describing a place in terms of a distance along a path or by two orthogonal distances from a place one removes uncertainty due to imprecise headings Choosing a reference point with small extent reduces the uncertainty due to the size of the reference point and by choosing a nearby reference point one reduces the potential for error in measuring the offset distances 52 To make it easy to validate a locality use reference points that are easy to find on maps or in gazetteers At all costs avoid using vague terms such as near and centre of or providing only an offset without a distance such as West of Albuquerque Table 1 In any locality that contains a named place that can be confused with another named place of a different type specify the feature type in parentheses following the feature name Data without locality information or only with doubtful details should be flagged as not possible to geo reference them with current information Vague Localities BAD Sacramento River Delta an extremely large
25. tencomitans actinomycetamcomitans Table 3 Result of non standard data entry for the valid species Actinobacillus actimomycetemcomitans source from Neil Sarkar uBio Project 4 1 Data cleaning Chapman 2005a shows that the cost of error correction increases as one progresses along the Information Management Chain Fig 2 and a manual process of data cleansing is also laborious time consuming and itself prone to errors Maletic amp Marcus 2000 Tools have to be developed for data cleaning and preventing of errors at their point of origin is the most cost effective method Tools are being developed to assist the process of adding geo referencing information to databased collections Such tools include eGaz Shattuck 1997 geoLoc CRIA 2004 BioGeomancer Peabody Museum n dat GEOLocate Rios and Bart n dat and the Georeferencing Calculator Wieczorek 2001 The most important point is that correcting problems and adding sufficient annotation for use should be done prior to not after publication of the data Data validation and annotation services should be done by the curator not after the data has been published and copies transferred When services are run against a copy of the data they need to be transferred and reconciled with the source copy increasing complexity and risking the introduction of new errors This approach will not apply to the many legacy datasets that are no longer curated so there will alw
26. tomatically by creating a new event The format for the date is DD MM YYYY hh mm ss With the buttons set Start and set End the current time will be filled into the adequate fields The collector the collecting method and remarks can also be added to each event 5 1 3 Species forms For each event a species list of observed or collected specimens can be created Therefore a species has to be selected on the page All Species Fig 7 from an authority species list dbf file This file can be created by researchers themselves and can be exchanged easily for using different species groups see 2 3 and 4 1 With the button Add the selected species will be transferred to the species list of this event For each species the sex and the number of observed collected specimens can be selected On the page Event Species Fig 8 all selected species are listed with information to the sex and the number of individuals The records can be removed by selecting one entrance and pressing the button Remove Selected Wrong entries of numbers can be corrected by choosing on the Page All Species the species which has to be corrected with the correct number of individuals After pressing the Add button the correction has to be confirmed and then the new number of individuals is saved specs cher ae x All Species a Event Sp_4 gt Event Species a Pictur 4 gt Acleris beramanniana 6 f Hellinsia osteodac
27. tylus 1 f Hellinsia osteodactylus 2 m Zeuzera pyrina 1 Abrostola asclepiadis Acalyptris platani Acanthophila alacella Acasis viretata Acherontia atropos Acletis aspersana Acleris emargana Acleris ferrugana Acleris forsskaleana Acleris literana Sex female v Number je v gt Remove Selected Remove All la Add ok x A Fig 7 List of all species that can be Fig 8 List of species for one event For selected For each species the sex and the each species the number of recorded number of individuals can be added specimens and their sex are available in brackets f female m male unknown 62 5 2 From field to the web The transfer of data from the field to the web environment via networks and portals such as BioCASE GBIF or WDPA http www wdpa org is necessary in order to provide global access to the sampled data Fig 9 All the records observations collected specimens or literature data have to be transferred to an online database that provides access for example through a wrapper for GBIF A wrapper is a piece of software that maps data contained in a local database to a common data exchange standard and then serves these data through standard exchange protocols This allows different databases to publish data to a network in a common form enabling integration and the development of common tools To integrate biodiversity data from
28. uarterjack Publishing see http www ishs org sci icracpco htm accessed 4 Oct 2009 67
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