PRECIS.pc Specimen database user guide

2005·8.1 MB·English

by  T. H. Arnold & H. M. Steyn

681.3.02
Button Functions
Help Buttons
Region Help Button Duplicate CAS Help Button
—SH — onthe Regions sub-form.Displays a onthe Specimen ID page. Displays a help
- screen explainingthe buttons onthat formwith instructions on howto dupli-
form
cate a record
Locality Keywords Help Button
onthe LocalityKeywords sub-form.
Displays a screen explainingthe buttons
onthatform
Form Operation Buttons
Exit Button \ Clear Form Button
+
C- Closesthe currentform orsubform and Clears informationfrom allfields on cur-
returnsto previousform rentform
Record Operation Buttons
First Record Button Save Record Button
Displaysfirst record in table >/ Saves currentrecord
Prior Record Button Undo Button
X
Displays priorrecord intable Returns record to its original state priorto
editing
Next Record Button
Displays next record intable ^ Remember Button
Remembers certain information,which
Last Record Button can be inserted in subsequentrecords
Displays last record intable
aa Find Button
Insert Record Button EPtI Allowsyouto searchfora specific record
+ Inserta newblank record
Flag Button
Delete Record Button Flags all records as having been checked/
Deletes current record undergone qualitycontrol
Edit Record Button
^ Places record into editmode, allowing
changesto be made
Other Operation Buttons
New Collector Button Write To File Button
1
Allows newcollector's nametobe Writes informationto afile
addedto'Collectors'table
Information Button
Insert Collector Button 1 Provides definitions ofterms ontheHabi-
Insertcollector(s) name remembered/ tats sub-form seeAppendix2
savedfromwithinthe Specimen Collec-
tors subform Specimen Count Button
Counts and displaysthetotal numberof
Preview and Print Button specimens inthe database
Allows information to be previewed
priorto printing Record Set Selection Button
To selecta range (subset) ofspecimensto
workwith
PRECIS.pc
National Herbarium, Pretoria (PRE)
Computerised Information System
SPECIMEN DATABASE
USER GUIDE
Trevor H.Arnold & Hester M.Steyn
MARY GUNN LIBRARY
0000014250
National
_Sou,t.hh AHtfrriican ulofc
Biodiversity
national
biodiversity
institute
S A N B
I
2005
Southern African Botanical Diversity Network Report No. 39
Citation
ARNOLD,T.H. & STEYN, H.M. 2005.PRECIS.pcSpecimenDatabase UserGuide. SouthernAfrican Botanical
DiversityNetworkReportNo.40. SABONET, Pretoria.
Address for Correspondence
PRECIS Information Manager
National Herbarium
SouthAfricanNational BiodiversityInstitute 661 3. 02. fjRKj
.
PrivateBagX101
Pretoria
0001 SOUTHAFRICA
Issued by
TheProjectCoordinator
SouthernAfrican Botanical DiversityNetwork
c/oSouthAfrican NationalBiodiversityInstitute
Private BagX101
Pretoria
0001 SOUTHAFRICA
Printed in2005intheRepublicofSouthAfricabyCapturePress, Pretoria, (27) 12349-1802
ISBN 1-919976-24-8
©SABONET.Allrightsreserved. Nopartofthispublication maybe reproducedortransmitted inanyformorby
anymeanswithoutthepermissionofthecopyrightholder.
TheSABONETProjectCoordinatorandtheAuthor(addressesabove)wouldappreciateeachreceivingacopyof
anypublicationthatusesthisreportasasource.
Technical editor: CeceliaBelgraverdeVos
Text design and layout:Antoinette Burkhardt, Pretoria, SouthAfrica(27)82888-8438.
Coverdesign: SandraTurck, Pretoria, SouthAfricanNationalBiodiversityInstitute, SouthAfrica(27) 12843-5000.
SABONETwebsite:www.sabonet.org
ThisreportisajointproductoftheNational Botanical Research InstituteofNamibiaandtheSouthernAfrican
Botanical DiversityNetwork(SABONET).Thesupportprovided bytheGlobal EnvironmentFacility(GEF)/United
NationsDevelopmentProgramme(UNDP)andtheUnited StatesAgencyforInternationalDevelopment(USAID)/
WorldConservationUnion-RegionalOfficeforsouthernAfrica(IUCN-ROSA)(Plotno. 14818LebatlaneRoad,
GaboroneWest,Extension6Gaborone, Botswana)madethisreportpossibleunderthetermsofGrantNo.690-
0283-A-00-5950. SABONETisaGEFProjectimplemented bytheUNDPandco-funded byUSAID/IUCN ROSA.The
opinionsexpressedhereinarethoseoftheauthoranddonotnecessarilyreflecttheviewsofUSAID,theGEF/UNDP,
the SABONETSteeringCommitteeorSABONETNationalWorkingGroups.
MARYGUNNLIBRARY 2
SCETHAFRICANNATIONALBIODIVERSITY!fJ5TmJII
;A. , PRIVATEBAGXICl
?M?': PRETORIA0CC1
REPUBLICOFSOUTHAFRICA
IUCN
national
biodiversity
institute TheWorld ConservationUnion
S A N B
I
Contents
Acknowledgements
viii
Introduction 1
Chapter 1. Installingthe MySQL service and specimen database 3
1.1 First-time installation : 4
2.11.2 Re-installation aftera system crash 15
1.3 Creating a Desktop shortcut 15
1.4Startingthe databaseforthefirsttime 16
Chapter 2. System overview 19
NewSpecimens 20
2.2 Existing Specimens 20
2.3 Reports 21
2.4Export/Import 21
2.5 Look-UpTables 21
2.6 Print Labels 21
2.7 Extract Records 21
2.8Local Settings 21
Chapter 3. New Specimens 23
3.1 Add Specimens 26
3.1.1 New Specimens: Specimen ID page 26
3.1.2 New Specimens: Collector(s) page 30
3.1.3 New Specimens: Localitypage 32
3.1.4New Specimens: Habitatpage 35
3.1.5 New Specimens: Description page 38
3.1.6New Specimens: Otherpage 43
3.2Transfer Batch 48
3.3TransferOne 48
3.4 PrintLabels 48
3.5 Delete Specimens 48
Chapter 4. Existing Specimens 49
4.1 Specimens: Specimen ID page 50
4.2 Specimens: Collector(s) page 54
4.3 Specimens: Localitypage 56
4.4Specimens: Habitatpage 59
4.5 Specimens: Descriptionpage 62
4.6NewSpecimens: Otherpage 66
Chapter 5. Reports 71
5.1 Mappit Output 72
5.2 No Grids 74
,
5.3 Not Checked 76
5.4Specimen Details 77
5.5 Species perRegion 80
5.6Accession Register 82
5.7 Species perGrid 83
5.8 Species List 84
5.9 Special/API Reports 85
Chapter 6. Import/Export 89
6.1 PRECIS 90
6.2 HISPID3 91
1
Chapter 7. Look-upTables (Data Dictionaries) 93
7.1 Authors 94
7.2 Biotic Effects 96
7.3 Collectors 97
7.4Colours (Flower/Fruit) 98
7.5 DetNames 99
7.6 Exposure 100
7.7 Families 101
7.8 Genera 102
7.9 Growth Forms 103
7.10 Habitats 104
7.11 Herbaria 105
7.12 Lithology 106
7.13 LocalityKeywords 107
7.14Materials 108
7.15 Moisture Regimes 109
7.16 Occurrence 110
7.17 Regions 110
7.18SoilTypes 112
7.19 Special Collections 113
7.20 Species 114
7.21 Substrate 117
7.22Type Categories 118
7.23 VegetationTypes 119
7.24Vouchers 120
Chapter 8. PrintLabels 121
8.1 Option 'N' (NewSpecimens) 122
8.2 Option 'E' (Existing Specimens) 124
Chapter 9. ExtractRecords 125
9.1 CopySpecimens 127
9.2View Specimens 129
9.3 Delete Specimens 129
9.4Print Labels 129
9.5Utilities 129
Chapter 10 Local Settings 131
.
Chapter 1 Backing upthe database 135
.
11.1 MySQL Backup and Restore procedure 136
11.2 Using "Copy"to backup and restore database 138
11.3Whatconstitutes a backup 139
11.4Howoftento backup 140
11.5 Backup storage location 140
References 141
Appendix 1. Database Help Buttons 143
Appendix 2. Definitions 147
Appendix 3. Specimendatabasetables 149
Appendix 4. Procedureforcapturingandstoringnewspecimendataandprintingspecimen labels...153
Appendix 5. Howthe SpmnDbfront-end linkstothe MySQL database 155
Appendix 6. Folderstructurewith importantfiles andtheirlocation 157
)
Appendix 7. AddingtheWinMySqlAdmintooltothe Startupand Start/Programs/SpmnDbfolders...159
1. Addto Startupfolder 160
2. Addto Start/Programs/SpmnDbfolder 160
Appendix 8. Where MySQL storesthe specimen database 161
Appendix 9. Usingthe reconstitute (recon.exe) program 163
Appendix 10. Creating a MS-Access SpmnReports database 167
1. Create SpmnReports database in PRECISfolder 168
2. Link SpmnReports databaseto MySQL SpmnData database and linktables 170
List of Figures
Fig. 1. MySQL software and Specimen database Installation Menu 4
Fig. 2. Stand-alone PC showingfourcomponentsto be installed 4
Fig. 3. Peer-to-peernetwork showing componentsto be installed onthe Serverand PCs 5
Fig. 4. Client/Servernetwork showingthe componentsto be installed on the Serverand PCs ...5
Fig. 5. MySQLServersand Clientsinstallationwindow 6
Fig. 6. MySQLServersand Clientsinstallation "Welcome"window 6
Fig. 7. MySQLServersand Clients installation "Information"window 7
Fig. 8. MySQLServersand Clientsinstallation "Choose Destination Location"window 7
Fig. 9. MySQLServersand Clientsinstallation "SetupType"window 8
Fig. 10. MySQLServersand Clientsinstallation "Setup Complete"window 8
Fig. 11. MySQL Connector/ODBCDriverinstallationwindow 9
Fig. 12. MySQL Connector/ODBCDriverinstallation "Welcome"window 9
Fig. 13. MySQL Connector/ODBCDriverinstallation "Readme!"window 10
Fig. 14. MySQL Connector/ODBCDriver"Start Installation!"window 10
Fig. 15. MySQL Connector/ODBCDriverinstallation "Finished!!"window 11
Fig. 16. MySQL Connector/ODBCDriverinstallation "Create ODBC Connection"window 11
Fig. 17. MySQL Connector/ODBCDriverinstallation "Create ODBC Connection"windowwithtwo
additional data entryfields 12
Fig. 18. SpmnDb Delphifront-end installation/setupwindow 12
Fig. 19. SpmnDb Delphifront-end installation "Welcome"window 13
Fig. 20. SpmnDb Delphifront-end installation "UserInformation"window 13
Fig. 21. SpmnDb Delphifront-end installation "StartCopying Files"window 14
Fig. 22. SpmnDb Delphifront-end installation "Setup Complete"window 14
Fig. 23. CreateShortcutdialogue box 15
Fig. 24. Selecta TitlefortheProgram dialogue box 16
Fig. 25. StandardKewHerbarium Code prompt 16
Fig. 26. Highestaccession numberprompt 16
Fig. 27. Herbarium labelheaderprompt 17
Fig. 28. Specimen Database menu 20
Fig. 29. NewSpecimens:Batch Headerform 24
Fig. 30. NewSpecimensdata entryform: Specimen ID page 26
Fig. 31. NewSpecimensdataentryform: Collectors page 30
Fig. 32. Collectorssub-form 31
Fig. 33. NewSpecimensdataentryform: Localitypage 32
Fig. 34. LocalityKeywordssub-form 34
Fig. 35. NewSpecimensdata entryform: Habitatpage 35
Fig. 36. Habitatssub-form 36
Fig. 37. NewSpecimensdata entryform: Description page 38
Fig. 38. Growth Formssub-form 39
Fig. 39. FlowerColours sub-form 40
Fig. 40. FruitColours sub-form 41
Fig. 41. NewSpecimens data entryform: Otherpage 43
Fig. 42. Special Collections sub-form 44
Fig. 43. Voucherfor: sub-form 45
Fig. 44. DuplicateDistribution sub-form 46
Fig. 45. TypeSpecimen of: sub-form 47
Fig. 46. Specimens dataentryform: Specimen ID page 50
Fig. 47. Specimens data entryform: Collector(s) page 54
Fig. 48. Collectorssub-form 55
Fig. 49. Specimens data entryform: Localitypage 56
Fig. 50. LocalityKeywords sub-form 58
Fig. 51. Specimens data entryform: Habitatspage 59
Fig. 52. Habitats sub-form 60
Fig. 53. Specimens data entryform: Description page 62
Fig. 54. Growth Forms sub-form 63
Fig. 55. FlowerColours sub-form 64
Fig. 56. FruitColourssub-form 65
Fig. 57. Specimensdata entryform: Otherpage 66
Fig. 58. Special Collectionssub-form 67
Fig. 59. Voucherfor:sub-form 68
Fig. 60. DuplicateDistribution sub-form 69
Fig. 61. TypeSpecimen of: sub-form 70
Fig. 62. Reports menu 72
Fig. 63. OutputforMappitform 72
Fig. 64. Formatofoutputfrom 'Print listofgrids' Mappit Reportoption 74
Fig. 65. SpecimenswithoutGridsform 75
Fig. 66. NewSpecimensnotcheckedform 76
Fig. 67. Specimen Detailsform 78
Fig. 68. Resultofa reportto generate specimen detailsforall specimens collected bya specific col-
lector 79
Fig. 69. SpeciesperRegionform 80
Fig. 70. Accession Registerform 82
Fig. 71. SpeciesperGridform 83
Fig. 72. SpeciesListform 84
Fig. 73. APIReportsform 86
Fig. 74. ListBarCodesforPrintingform 86
Fig. 75. XML outputform 87
Fig. 76. Import/Exportmenu 90
Fig. 77. PrecisImport/Exportmenu 90
Fig. 78. Look-Up Tablesmenu 94
Fig. 79. Authorsform 95
Fig- 80. BioticEffectsform 96
Fig. 81. Collectorsform 97
Fig. 82. Colours (Flower/Fruit)form 98
Fig. 83. DetNamesform 99
Fig. 84. Exposureform 100
Fig. 85. Familiesform 101
Fig. 86. Generaform 102
Fig. 87. Growth Formsform 103
Fig. 88. Habitatsform 104
Fig. 89. Herbariaform 105
Fig. 90. Lithologyform 106
Fig. 91. LocalityKeywordsform 107
Fig. 92. Materialsform 108
Fig. 93. MoistureRegimesform 109
Fig. 94. Occurrenceform 110
Fig. 95. Regionsform Ill
Fig. 96. SoilTypesform 112
Fig. 97. Special Collectionsform 113
Fig. 98. Speciesform 114
Fig. 99. CurrentName sub-form 116
Fig. 100. Substratesform 117
Fig. 101. Type Categoriesform 118
Fig. 102. Vegetation Typesform 119
Fig. 103. Vouchersform 120
Fig. 104. Example ofa PrintLabels Preview 123
Fig. 105. ExistingSpecimens:Batch Headerform 126
Fig. 106. CopySpecimenstobatch sub-form: Stage l 127
Fig. 107. CopySpecimenstobatch sub-form: Stage2(Selection byCAS) 127
Fig. 108. CopySpecimenstobatch sub-form: Stage2(Selection byFamily) 128
Fig. 109. Utilities sub-form 130
Fig. 110. LocalSettingsform 132
Fig. 111. PRECIS Specimen databaseMaintenance Menu 136
Fig. 112. Windowshowing contents ofBackupfolderwith eightfiles created bySpmnBackup
program 136
ACKNOWLEDGEMENTS
Acknowledgements
WethanksouthernAfrican botanistsfortheircomments and suggestions onthe design ofthe database.
Compiled by
T.H. Arnold and H.M. Steyn
South African National BiodiversityInstitute
Private BagX101
Pretoria
0001
Database design
TrevorArnold and Carole deWet
SouthAfricanNational BiodiversityInstitute
Private BagX101
Pretoria
0001
Database development
Carole deWet
SouthAfricanNational BiodiversityInstitute
Private BagX101
Pretoria
0001