Brahms Living Collections
Brahms Living Collections
Brahms Living Collections
Oxford Botanic Garden April 2011 - looking towards Magdalen College tower
CONTENTS
INTRODUCTION .......................................................................................................................................................... 3 GETTING STARTED ...................................................................................................................................................... 4 ACTIVATE MODULE .............................................................................................................................................................. 4 OPTIONALLY IMPORTING SETUP FILES ...................................................................................................................................... 4 SMALLER CUSTOM LOOKUPS .................................................................................................................................................. 4 ACCESSION BACKLOGS AND DATA TRANSFERS ............................................................................................................................ 4 EDITING LIVING COLLECTION RECORDS IN BRAHMS ................................................................................................... 5 EDITING IN DATA GRID MODE ................................................................................................................................................. 5 EDITING IN DATA FORM MODE ............................................................................................................................................... 5 LINKING ACCESSIONS TO LOCATIONS ........................................................................................................................................ 6 EDITING ACQUISITION DETAILS ............................................................................................................................................... 7 IDENTIFICATION AND ADDING SPECIES DETERMINATION ............................................................................................................... 7 VOUCHERS AND ADDING LINKS TO SPECIMENS ........................................................................................................................... 8 BOTANIC GARDEN ZONES AND LOCATIONS ................................................................................................................ 9 EDITING THE MAIN LOCATIONS FILE ......................................................................................................................................... 9 MERGING LOCALITIES ........................................................................................................................................................... 9 CREATING LOCALITY GROUPS (TAG PROFILES) .......................................................................................................................... 10 IMPORTING LOCATION NAMES.............................................................................................................................................. 10 FIELD LIST BOTANIC GARDEN LAYOUT .................................................................................................................................. 10 STOCK-CHECKS AND OTHER EVENTS ..........................................................................................................................12 FIELD LIST LIVING COLLECTION EVENTS................................................................................................................................. 13 RDE AND LIVING COLLECTIONS ..................................................................................................................................14 RDE INTRODUCED ............................................................................................................................................................. 14 USING RDE TO ADD LIVING COLLECTIONS ............................................................................................................................... 14 USING RDE TO ADD STOCK-CHECKS AND OTHER EVENTS ........................................................................................................... 15 MANAGING SPECIES NAMES AND RELATED DATA .....................................................................................................17 IMPORTING EXISTING TAXA LISTS........................................................................................................................................... 17 THE MAIN TAXA FILES ......................................................................................................................................................... 17 SPECIES DESCRIPTIVE TEXTS ................................................................................................................................................. 17 ADDING AND EDITING NAMES .............................................................................................................................................. 18 CONTACTS, SUPPLIERS AND OTHER ADDRESSES ........................................................................................................19 EDITING CONTACTS ............................................................................................................................................................ 19 FIELD LIST CONTACTS AND ADDRESSES ................................................................................................................................. 19 IMPORTING NAMES/ADDRESSES FROM AN EXTERNAL FILE .......................................................................................................... 20 QUERYING LIVING COLLECTIONS AND GENERATING REPORTS ..................................................................................21 QUERYING ....................................................................................................................................................................... 21 REPORTS INCLUDING LABELS ................................................................................................................................................ 22 FIELD LIST LIVING COLLECTIONS ..............................................................................................................................23
Introduction
The Living Collections module is designed for botanic gardens and other projects wishing to track data and images for individual plants. The module benefits from all standard BRAHMS features with options to view, edit, query, report, map, export and publish online. There are also tools to sort, filter, calculate, tabulate and analyse data in numerous different ways. Living collection accession records include a description of the accession in the garden, how it arrived and from where, the original source of the material, identification and vouchering. Documents such as PDF files can be linked to records, an example would be a material transfer document . A history of management events including standard garden stock-checks, name changes, propagation, plant movement and others is also be maintained. Botanic Garden localities can be described in detail with pinpoint map locations linked to botanic garden areas and theme zones. Images of living plants, their original habitat, linked specimen vouchers and others can be linked to all records. Images of botanic garden localities may also be stored. Individual projects can extend the standard living collection data structure by editing the living collections linked data file an appendix to the standard file. The module is fully supported by Rapid Data Entry which can be used to capture new data, data backlogs and data transferred from other formats such as Excel worksheets. RDE can also be used to upload stockchecks in batches. The living collection module is linked through to the main BRAHMS taxonomic framework. Thus detailed information can be stored about individual taxa from plant order through family and genus to infra-specific level s (cultivars and hybrids included) as appropriate. Species details may include synonymy, common names, descriptions, known distribution, conservation status and more. Equally, there are links to the main BRAHMS geographic framework allowing the storage of plant origin details. Voucher specimen links can be added with links through to the main botanical records file. Vouchers may be from the original wild collection or taken from established garden plants. Thus, data and images from herbaria and living collections can be united and streamlined in a single database. You can design your own website directly from BRAHMS using WebConnect and upload details about your accessions so these may be queried online. See http://dps.plants.ox.ac.uk/bol/content/documentation/BRAHMSWebConnect.pdf. The BRAHMS training guide, while not explicitly dealing with living collections, provides all the necessary background information you need to install BRAHMS, log in and get started with RDE and BRAHMS itself. See: http://dps.plants.ox.ac.uk/bol/content/documentation/BRAHMStraining2010.pdf. This module has been prepared with inputs from Gerda van Ufflen (Leiden) and Alison Foster (Oxford). Some fotos provided by Gerda van Ufflen.
Getting started
Activate module
First ensure that the living collections module is included in your menu selection using Utilities > My setup/profile >Active modules
A sample data grid with a data field view selected (supplier data) Lookup options can be used for all the relevant fields. Some lookups refer to standard BRAHMS lists (e.g. species, places, collector names, botanic garden localities and supplier names). Others link to smaller custom lookup lists which you can define and standardise for your project. Examples are living collection status, habit and material supplied as. The fields available in the main file (and thus on the data form) are listed at the end of this document.
The living collections data form with the Events tab selected
To change the determination of an accession, open the form and go to the Identification tab. A standard lookup (right-click or F9) on any taxon field in the main living collections file will auto-open the form on the Identification tab.
If the species in not in your species file, you will need to add that first. Refer to the section on managing species names and related data in this document. When you change a determination of an accession, an entry is auto-added to the events file to record the old and new species names, the date of the change and the name of the person making the change.
Accession determination changes are auto-registered as an event for the edited record.
Snapshot of the locations file. The field LVTOTAL (total living collections linked to an area is updated using Calculate > Update calculated fields.
Merging localities
Not uncommonly, dictionaries such as the garden locations file can build up 2 or more separate entries that represent the same entity. For example, you may have a botanic garden locality Alpine House and another entry called Alpine glass house and these may represent the same place. There may be yet further entries such as Alpines and Alpine glass houses. Ideally, you would simply delete the entries you do not want, keeping the one you prefer. However, you cannot delete an entry if it has accessions linked to it in your database. The trick here is to merge the wrong entries into the correct one using the MERGETO field and the record ID numbers. Merging is activated by select Edit > Merge records. Using MERGETO is described in more detail in the manual.
Two records are being merged here into the (correct) record with ID 171 called Alpine Frame
b) From the Events tab on the main Living Collections editing form. Events are updated as you move from record to record.
An example RDE file screen. In RDE, data are entered into an external DBF file. Once checked, these data are easily transferred into your main database. RDE file structure is very flexible you can add and remove columns to suit your project.
The RDE data can also be edited using a form. Use F3 or click on the
You can then freely add data to this file. When the data are transferred to BRAHMS, the event(s) will be added in and linked to the accession number you enter in the ACCESSION field. Use F9 to look up accession numbers. You may want to update a species name, garden location, the accession status or simply add a free text note. However, if you are adding events to a group of accession records already in your database, a better procedure will be as follows: a) From your main database, extract the living collections you want to add or edit events for. For example, if you wanted to do a stock-check/inventory of all plants in a selected garden area or glass house, extract these accessions. Remember, a very flexible way to extract records is to use the Tag method: tag records in your main living collections file and then select Living collections > Extract/Query data and choose Tagged. b) In the opened extract file, select Tools > Create events/Stock-check RDE file for tagged This will create your RDE file and register it in the living collections RDE manager, ready to open and edit.
Part of an events RDE file created for AF (Alpine Frame). The file is pre-populated with data, ready to edit prior to transfer to BRAHMS.
Snapshot of a species file Details on how to extend the structure of your species file, adding non-standard fields to the species link file are explained in the guide and manual. Examples are adding new fields to store text notes as below.
Some of the text items added to the Conifer database species file. Text entries can be formatted into reports. For botanic garden databases, details about uses, common names, natural distribution and name origin may be useful. All of the information you choose to store in your taxa files can be drawn upon when creating living collection reports.
Country name Telephones and fax numbers Email address Website link Notes
Extract files are normally created when you want to prepare outputs and reports, for example general lists, labels, a determination list, a map, a checklist, an index to collections, a species list , etc. Select Living collections > Extract/Query data to open the extract form and choose one of the search options. Extracting tagged records can be used with flexibility to query almost any group of records. In the query form shown here, records are being queries by a botanical garden locality group (All glass houses) created by this project.
An extract of Bromeliaceae, filter applied to show living plants, fast-sorted by species. The been used to tally up the number of records per species.
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Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant origin Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Plant location Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification Identification
ALT2 ALTRES ALTTXT LOCNOTES HABITATTXT COLLECTORS ORIGINNOTE NUMBER COLLDD COLLMM COLLYY BGLOCATION BGZONE BGTYPE BGLAT BGNS BGLONG BGEW BGLLUNIT BGLLRES XCOOR YCOOR GROWNIN PLANTCOUNT BGLOCNOTE FULLNAME GROUP ORDER FAMILY GENUS SECTION TAXSTAT HYBRID CF SP1 AUTHOR1 RANK1 AUTHOR2 SP2 RANK2 SP3 AUTHOR3 DETBY DETDD DETMM DETYY DETCAT DETNOTES DETSTATUS
Material origin: maximum altitude of location Material origin: altitude resolution code Material origin: altitude text Locality notes Habitat description collector names(s) Material origin notes Collectors field number Collection day Collection month Collection year Garden location Garden zone Garden category/zone Latitude of plant in garden NS for BGLAT Longitude of plant in garden EW for BGLONG Map units for BGLAT/LONG Resolution coding for BGLAT/LONG Alternative X coordinate of plant in garden Alternative Y coordinate of plant in garden Grown in Plant count Garden location notes Calculated species name (combines genus + sp1 fields and optionally authors) family group (stored in family file) Order name (stored in family file) Family name (stored in family file) Genus name (stored in genus file) Section name (stored in species file) Tax status of species (acc, syn, etc.) NB: available in all taxa files. Hybrid yes/no Used to indicate doubtful species - not to be confused with DETSTATUS 1st species epithet Author for SP1 Rank of SP2 (ssp. var, f., etc) Author for SP2 2nd species epithet Rank of SP3 (ssp. var, f., etc) 3rd species epithet Author for SP3 Detby name (who named material) Det day Det month Det year Det category Det notes Detstatus (used this rather than the species file CF field to indicate doubtful dets)
Identification Identification Identification Identification Identification Events Events Events Events Events Events Labels Labels Labels Labels Propagation Propagation Propagation Propagation Propagation Propagation Voucher Track -
HARDINESS IUCN STAR CITES COMMON EVENTCAT EVENT EVENTDATE EVENTEND EVENTNOTES EVENTSUM LABELRANGE LABELDATE LABELNOTES LABELPRINT BREEDING CROSSCLONE PARENT1 PARENT2 PARENTINFO SEX VOUCHNOTE EDITHIST IMAGELIST GAZCODE SPNUMBER BRAHMS ENTRYDATE MYDOCS IMAGES RDEFILE WHO
Hardiness coding IUCN conservation coding STAR conservation code as used widely by Oxford CITES A selected common name (other can be stored in common name list) Event category (stock-take, sowing, re-plant, sprayed, plant death, etc) Event title Event date Event end date Event notes A calculated sum of events for this accession Species range (concise) Garden label last printed Additional label text Label needed yes/no Notes on plant breeding Propagation Parent1 Parent2 Propagation notes Sex Notes about voucher. All other fields on the Voucher tab are picked up from a linked specimen BRAHMS-generated: field used to keep track of edits RDE field for adding images file names BRAHMS-generated: link to gazetteer and other geo files (plant origin) BRAHMS-generated: link to species and other taxa files (material ID) BRAHMS-generated: ID link to a botanical record for vouchering etc. BRAHMS-generated: date record added to database Calculated field: number of linked documents (PDF files, etc) Calculated field: number of linked images BRAHMS generated - origin RDE file name for imported data BRAHMS-generated: coded ID of data entry person