HISPID3

Herbarium Information Standards and Protocols for Interchange of Data

Version 3

Editor
Barry J. Conn



Internet URL
http://www.rbgsyd.gov.au/HISCOM

© Council of Heads of Australian Herbaria

Previous Versions of HISPID

Version 1:

Croft, J.R. (ed.) (1989). HISPID - Herbarium Information Standards and Protocols for Interchange of Data (Australian National Botanic Gardens: Canberra).

Version 2:

Whalen, A. (ed.) (1993). HISPID - Herbarium Information Standards and Protocols for Interchange of Data (National Herbarium of New South Wales: Sydney).

As with all previous versions of HISPID, the preparation of the HISPID3 interchange standard is being coordinated by a committee of representatives from all major Australian herbaria. Since 1995, the development of this standard has been coordinated by the 'Herbarium Information Systems Committee' (HISCOM) (refer Internet URL http://www.rbgsyd.gov.au/HISCOM).

INTRODUCTION

The 'Herbarium Information Standards and Protocols for Interchange of Data' (HISPID) is a standard format for the interchange of electronic herbarium specimen information. HISPID has been developed by a committee of representatives from all major Australian herbaria. This interchange standard was first published in 1989, with a revised version published in 1993.

HISPID3 is an accession-based interchange standard. Although many fields refer to attributes of the taxon they should be construed as applying to the specimen represented by the record, not to the taxon per se. The interchange of taxonomic, nomenclatural, bibliographic, typification, rare and endangered plant conservation, and other related information is not dealt with in this standard, unless it specifically refers to a particular accession (record).

This data dictionary is concerned primarily with data interchange standards but has considerable relevance to database structure since the task of preparing interchange files is simplified if the data fields of the despatching and receiving databases match, as far as possible, the interchange standard. If differences do exist then, generally, it is easier to combine data fields than it is to dissect them in a reliable manner. Fields that are concatenated are frequently heterogeneous in their nature and many preclude the possibility of rearranging the data contained within such fields.

The fields discussed in this data dictionary cover most of the herbarium and botanic gardens sphere of activity and have been arranged in groups of similar types of information. In many cases these groups may coincide with separate well­defined tables (or databases) of structurally similar records.

The challenge for herbarium data managers is to decide whether the data are to be efficiently exchanged as discrete but related tables (databases) or as a larger single flat file that may have to be appropriately dismembered by the receiving institution. Some database packages are able to stack multiple values in a single field. This useful data structure complicates the interchange format and will not be used at this stage.

Format of HISPID3

The 'Herbarium Information Systems Committee' (HISCOM) considered several format options for HISPID3. It was agreed that the interchange format of HISPID3 would be a flat­file. This flat­file format was chosen because it was relatively simple and required minimal computer programming to enable the importing and exporting of data. Furthermore, this format was in agreement with that chosen for the 'International Transfer Format for Botanic Garden Plant Records (Version 2.00)(ITF2). Although, it was recognised that it was difficult to transfer relational (hierarchical) data in flat­file formats, it was decided to proceed with the publication of this version of HISPID so that electronic data interchange could be actively encouraged. It is hoped that future versions of HISPID will include the capability of transferring data such that the relational structure is maintained.

There have been several major changes incorporated into this version of the HISPID transfer format, namely:

(1) HISPID3 allows for the interchange of variable length fields. It is no longer restricted to a fixed length format.

(2) HISPID3 allows missing data to be omitted from the transfer file

(3) HISPID3 provides a protocol for interchanging (non-standard) data that are either not defined within this document or are in a form different to that define here.

(4) Apart from a few exceptions, HISPID3 does not evaluate the relevance of interchanging any of the specific fields described in this document

(5) The references to how data are stored in the major Australian herbarium databases has been deleted from this document

(6) HISPID3 has been developed in conjunction with ITF2 (International Transfer Format for Botanic Gardens Plant Records version 2.00) so that the two interchange standards are as compatible as possible.

The transfer format of HISPID3 is based on 'Information technology - Open Systems Interconnection - Specification of Abstract Syntax Notation One (ASN.1) '. International Standard ISO/IEC 8824, 2nd ed. (1990)(ISO/IEC: Genève).

Definitions

• A HISPID3 file is the total contents of the information transferred. Each file begins with the file identifier 'startfile' and ends with the file identifier 'endfile' . Additional file header information is provided before any of the record data.

• A HISPID3 Record includes all data associated with a single Accession Identifier included in the overall file. Each record begins with the opened brace character '{' and ends with the closed brace character '}'.

• A HISPID3 field is the basic unit of information. The data of any record are grouped into several separate fields of information. Each field is prefaced by a unique field identifier. If the information pertaining to a certain field is to be interchanged, then the appropriate unique field identifier must be interchanged with this information. Each field is one line long and is always terminated by a comma (,). The data within alphanumeric (text) fields are enclosed (delimited) by double quotation marks ("), whereas numeric fields are not enclosed by double quotation marks. Fields are either 'required' for transfer in a HISPID3 Record (in which case a HISPID3 record is incomplete if one of these fields are excluded) or are 'optional'. For example, the 'Institution Code' field and the 'Accession Identifier' are always required in any valid HISPID3 record.

As far as practicable, raw data should be used. Interpretations or corrections in free text fields should be enclosed in square brackets: '[' and ']'. Omitted data should be represented by the ellipsis: '...'.

Italics:

Since the printable ASCII (EBDIC or UNICODE) character set does not include italicised characters, these are not included in the interchange file.

Nulls:

If information is not known for a field, then the field need not be included in the interchange file or else the field identifier may be interchanged unfilled. However, if the value of the Collector's Identifier field is unknown, then the default value should be 's.n.'.

Single character fields:

In general, single character (flag) fields have not been included in this standard because of the difficulty of detecting data entry errors.

Codes:

As for the 'single character' fields (above), codes are mostly not included in this standard because of the difficulty of detecting data entry errors.

Relevant Standards

The fields included in this interchange standard are a compilation from the following sources:

ABIS Australian Biotaxonomic/Biogeographic Information System

(Australian Biological Resources Study ­ ABRS)

ICBN International Code of Botanical Nomenclature

(International Association of Plant Taxonomists ­ IAPT)

ITF International Transfer Format for Botanic Gardens Plant Records

ITFBGPR (Botanic Gardens Conservation International ­ BGCI)

ITRF International Earth Rotation Service Terrestrial Reference Frame

MFN Minimal Functional Nomenclator, also known as:

DSTI Database Standards for Taxonomic Information

(Taxonomic Database Working Group ­ TDWG)

PECS Plant Existence and Categorisation Scheme, also known as:

POSS Plant Occurrence and Status Scheme

(World Conservation Monitoring Centre ­ WCMC Threatened Plants Unit - TPU)

SDTS Spatial Data Transfer Standard

TDWG Taxonomic Database Working Group

TLR Type and Lectotypification Registers

(Taxonomic Database Working Group ­ TDWG)

WGSUB World Geographical System for Use in Botany

(Taxonomic Database Working Group ­ TDWG)

XDF Language for the Definition and Exchange of Biological Data Sets

(Taxonomic Database Working Group ­ TDWG)

Summary of the important features of a HISPID3 file:

a) Each field is prefaced by an unique identifier this refers to the fields which describe the contents of the file, as well as to those which describe the information contained in each record);

b) Each unique identifier must begin with a lowercase letter (a-z) and cannot contain any spaces;

c) A transfer file begins with the file identifier 'startfile';

1. Each record begins with the opened brace character '{';
2. Each record ends with the closed brace character '}';

f) Variable length fields are allowed;

g) Fields can be omitted from the transfer file if there is no information available for that field;

h) Alphanumeric data are enclosed by double quotation marks (");

i) Numeric data are not enclosed by double quotation marks;

j) Each field and each file information is one line long and is terminated by a comma (,);

k) Each transfer file ends with the file identifier 'endfile'.

Example of the start and end of a HISPID3 file:

An example of a filled HISPID3 interchange file

FORMAT OF THE TEXT IN THIS DESCRIPTION OF A HISPID3 FILE

The herbarium data fields for information interchange are listed below in the following format:

The full field name:

The name of the discrete piece of information within the file or within each record.

The transfer identifier code:

The standard codes used as file or field identifiers in the transfer file.

TDWG Short name:

A short, meaningful­sounding single­word name for the field, proposed by TDWG.

The field description:

A general elaboration of the field name.

Relevant standards:

The existence of this type of data in any other published or proposed biological standards.

Domain/Range/Values:

The type of data allowed in this field, the range of values, or individual allowable values, and capitalisation.

Comments:

Any other remarks on the use or application of these data and its relationships to other data. Any conflicts or problems in the application of these data types.

Rules:

Additional information to that provided in Comments explaining the rules applying to these data.

Notes:

Additional comments to those provided in Comments and Rules