Indo-Pacific Mollusc Checklist

Protocol for data entry to BioLink

I. General considerations before you start.


When you are using the Reference Database, NEVER Delete any references, even if there are two or more copies of the same reference. The taxa in the database are linked to a REFERENCE CODE and if you Delete a Reference you are deleting a link as well!

I believe this goes for the Journal Picklist as well. If you delete a Journal because it is replicated, you are removing a link or many links.

Never delete Keyword Types or Values, or other pick lists. If you think some part should be changed or words added contact Paul Morris (

Never move any taxon from one place to another without checking that the literature you have is more recent than the literature that was used when the last person accessed the taxon.

Always search the database for the taxon you are about to enter, unless you are sure you are the first to enter that taxon name. If you search for eg. a family name and the name comes up twice, you will have to use the one that stem from AMS, as that is more complete than the ANSP import at the moment. The ANSP import only contains valid names with no information attached. (This should change shortly when the two databases are merged properly).

Because BioLink erase previous searches you will have to use the Taxon Explorer Contents to keep you tree open, and use Taxon Explorer Find to search for the individual taxa you are adding.


When you attach a reference to a taxon name you will have to be certain that it is the right reference. Many authors have published papers consecutively after each other in a volume of a journal, and it may not be enough to know Author, Year and Volume. If you have the Page on which the taxon was described, then it should be possible to find the right reference.

Some publications have been published after they were read before a society and will have publication dates later than the year stated on the publication. You can check in your library for older literature, but this may not be enough. Many Bibliographies of Authors have been compiled from AMS and if your date is different from the date in the reference database (the former generally earlier) then you should adhere to the reference database date, unless you have better data. Please email Peter Middelfart ( if you are in doubt.

Many old books were published over several years. These books may be listed in the reference database in full with the first year of publication, and/or as separate parts with the page range published in each year. You should try to find the exact year that the taxon was published and attach the exact book part. If you cannot do that, you may choose the whole book with a qualification note regarding date.

If you are uncertain about the reference you have, generally because you only have it from a secondary source and not in full, you should:

1. Try to search your library for the reference in full, or

2. E-mail another partner in the project for help.

Do not enter the reference as new and incomplete except when all other options fail. If you have to enter a reference in part, you will have to put <***> in the Title so we can extract this reference later for more extensive searches. If you are missing a small part like initials, volume, page range etc. then you should use the same symbol.


We are concentrating on the Indo-Pacific. We are excluding the north Pacific (Arctic), south Pacific (Antarctic) and south Indian Ocean (Antarctic). For the time being we are also excluding New Zealand (checklist done) and Japan (checklist done).

ANSP is compiling faunal lists from the Western Indian Ocean, Central and Eastern Pacific.

AMS compiles faunal lists from Central Indian Ocean east to Western Pacific.

If AMS or ANSP compiles Revisions then taxa FROM ALL AREAS OF THE INDO-PACIFIC (see above) should be compiled. This is to speed the compilation process up, as one publication only need to be visited once.

II. Practical approach

The suprageneric level

You may enter new suprageneric taxa if appropriate, or move entire generic or subgeneric taxa between these higher taxa, if you are certain that you are using the latest literature references to do this.

You only need to enter a minimal amount of information in this category. The Reference Link of these higher taxa will be supplied by MNHN, but you do need to enter the Available names for MNHN to search on. MNHN does not necessarily have the synonymies, so we will have to use those of the revisions used!

You will have to enter the revision and/or faunal list you have used to compile a higher taxon, under the Valid Name References. Use the Notes tab to indicate where the compilation is up to, eg. <Australian taxa compiled, from {REFERNCECODE1}, {REFERENCECODE2}, etc. by peterm at AMS; extra-Australian distribution not compiled in detail>.

The higher taxa that have been compiled to date DO NOT have this information. A list of families that have been dealt with and the literature used will be compiled shortly. Until then you should COMMENCE WITH CAUTION.

If you are in doubt about the Status, you should contact the person who modified the group the earlier.

The Genus Level

1. Add the Genus Valid Name to the higher taxon.

2. Add list of Available Names to the Genus Valid Name.

3. Apply data. You should Apply frequently as BioLink has a habit of freezing occasionally no matter how cautious you have been.

4. Edit Taxon Name for each genus available name and remove ticked "Details are verified" unless you have the original description of the genus name in front of you. Click OK.

NB! This procedure will probably be changed later when an upgrade of BioLink becomes available, until then we will have to live with the problem.

5. Edit Taxon Detail for each Genus Available Name.

6. Click the reference selection button to select a proper reference for the genus, and add the proper page reference. If you are not sure which reference to use ie if you reference is incomplete, leave the reference open, but add to the Qualification field the data you have. The Paris team will clean this up later.

NB! If the Genus Available Name data has been accessed by the Paris Team (see the Ownership tab before commencing) then leave as is, unless you are certain you have data that will add to the completeness of the Available Name.

7. The Qualification field may be used for messages that can be upgraded later. But remember that this information may not be accessed before public access to the database, so keep the text clean and correct.

8. The "real" purpose of the Qualification field is for adding taxonomic qualifications for the name. Follow the ICZN.

9. THIS STEP IS ESSENTIALL THE RESPONSIBILITY OF MNHN. Access the Type Species folder if applicable, ie if the genus has a type species, and enter the type species as a text string with the species name in italics (ctrl - i). Many of the Genotype Names already present may not be italicised because of import problems. You will have to italicise these.

Remember to use the original combination of the species!

The "Method of Fixation" needs to be selected from the list. Follow the ICZN. If you do not know the Method of Fixation, leave blank.

If the name is a replacement name click None Required. If no type has been designated and the name has been referred to as containing a number of species click that field. The type species selecting tab will become unavailable and you will have to enter the species included. If no species have been included click that button. The species selection and type species tabs will become unavailable.

10. THIS STEP IS ALSO THE RESPOSIBILITY OF MNHN. If you have a reference in front of you that deals ONLY with the name you have just entered or a selection of the total number of available names in the synonymy list you will have to enter the reference under this available name / and the rest of the selection as well. If the reference you have cover all the available names in synonymy you can enter the reference under the Genus Valid Name as a Synonymy Reference.

11. All other tabs should be left untouched.

12. Click OK, and continue with the rest of the available names.

13. Go to the Valid Name and access Valid Name Detail.

14. Enter a Common Name for the Genus and attach a reference if available. We should not be inventing Common Names at this stage. If there are several Common Names for the Available Names, now synonymised, then all should be entered with the Note <for Taxon Name Author, Year>. If there are several common names by various authors, then they should all be entered with the proper references attached.

15. Under the Reference Tab all references used should be entered, together with important sources you might not have seen. This might be an old reference like Reeve's monographs, which you might not have access to, but which have substantial information about many genera. If your reference only contains information regarding eg. Synonymy, then the reference should be entered with the Type Synonymy. If the reference contains more information than just synonymy, then this reference should be of the type <General Reference> but with the Qualification: <Synonymy, Description, Key, Distribution, Phylogenetic analysis, Fossil history etc. etc>. Any single reference should not be entered several times with different types because this takes too long.

16. The only other Tab to access at the Genus Valid level is the Keyword Tab. If the genus shares a common feature, eg. <infaunal>, then that information should be entered here, avoiding duplication of entry under each species of the genus. The reference where this information stems from should be entered under the Reference Tab.

NB! All other Tabs should be left untouched. Some information in these fields will be cumulative information from the species level, and this cannot be done until all areas have been dealt with by all Partners in the project.

17. Once you have entered the Genus Valid Name information and you have used the most recent literature you should access the Edit Taxon Name and tick the Verified box. This indicates that this Valid taxon is finished!

The Species Level

1. Add the Species Valid Name under the Genus Valid Name.

2. Add all Species Available Names to the Species Valid Name.

3. Add important New Combinations, mispellings, misidentifications as Literature Names. They should be added as <Taxon Name auct.>

Only use combination changes at the genus level as New Combinations.

Avoid entering mispellings unless these have been used consistently in the literature.

Only add misdentifications when these misidentifications have been consistently used, and duplicated in the literature.

4. Apply the entered combinations. If the Synonymy list is long it is advisable to Apply a few times throughout the process of entering the synonymy list to avoid loosing data.

5. Edit Taxon Name for each Available Names to un-tick the Verified box.

NB! This problem will be changed in a later version of BioLink.

6. Edit Taxon Detail for the Available Names.

7. Locate the proper reference in the Reference Database and attach it to the taxon. Add page, plate and figure reference in the page field.

When giving the page of a description, use the page number on which the description begins, not the page range of the whole description, eg the description for Pinna bicolor is on page 204, not pages 204-206.

The Qualification field should be used in accordance with ICZN rules. You may enter illustration references in this field. Many of Linnaeus names referred to illustrations in earlier taxonomically unavailable works. You may refer to one of these, if one has been chosen in the Secondary Literature you are using.

Manuscript names need to go into the qualification field in square brackets: [ex author, date, reason] eg. [ex Hanley, MS]

8. Add type information in the Type Date Tab. Select Primary Type and enter the information you have regarding this type. Do not enter Secondary Type data as that is beyond the scope of this project. If you have the information for Secondary Type available add that under the Reference Tab as a Type Data reference.

9. If the name you have for the synonymy is from a list, which contains the synonymy in part, you should add the Secondary Source under the Available Name and Valid Name References. If the Secondary Source contains all the available names in your synonymy then you only need to add the Secondary Source at the Valid Name level.

10. Click OK

11. Edit Taxon Detail for the Literature Names. The reference you will have to attach here is normally the first occurrence of a New Combination. Other subsequent usages of that combination does not belong here, but may be entered under the Valid Name with the Qualification (as <new combination name>). If you are not sure if the reference you have is the earliest reference to the changed combination, then just enter it anyway. If an earlier reference is discovered later this will be changed.

If you have a reference for a misidentification, you may attach the reference to that literature name, with the qualification <misidentification; not Taxon Name Author, Year>. If only PART of the material described/illustrated was misidentified you may indicate this by using <misidentification, in part; not Taxon Name Author, Year>.

The remaining information of this reference may be entered under the taxon it was identified as, either as a literature name, if appropriate, with the qualification <in part> or as a General reference under the Valid Name with the same qualification.

12. Click OK to save the Literature Name Detail.

13. Edit Taxon Detail for the Species Valid Name.

14. A common name should be given with a literature link and page. If two or more taxa have been merged and two or more Common Names are available, you should enter them all with the appropriate references, and the qualification <for Taxon Name, Author, Year>. Use only Original Combination for the Taxon Name, except if you do not have it available.

15. Go to the Reference tab. Click Add New and select the type of reference you are about to enter (see below), click OK. Select a reference from the Reference Database, and enter the page, plate(s), fig.(s) etc. In the Qualification field you may enter the name used by Author <as Taxon Name Author, Year>. If you want to add extra information do so by eg. <as Taxon Name Author, Year; Physiology, Biology, Ecology, Reproduction, Distribution and Habitat>. If only part of the taxon in the reference you have was correctly identified you should add <in part, as Taxon Name Author, Year; etc.>.

If the reference you have is a Single Type, ie. only covers one field eg. Biology, then you may attach the Type <Biology> to the reference from the list. If your reference covers two or more Types of references, then you may add that information in the qualifications field, and leave the Type of that references as <General Reference>.

It is important that the information used in the Distribution and Keywords Tabs, is indicated here. So, if you have used Distribution data from a particular reference, that reference should have the Type <Distribution> linked to it or listed in the Qualifications field.

16. Go to the Distribution tab. Write the exact distribution as listed in the source you have in front of you, in the text field. From the Region Explorer select the regions from the <World (Standardised Hierarchy)>. Keep adding areas until the text in the text field above fits the selected areas.

17. Go to the Keywords tab. Click Add New and select a Keywords Type (see the list from the meeting at ANSP). Click OK. Click the select button for a Value of the Keyword Type. Click OK. You may add a Qualification to the Keyword information. This has to be done for Depth Zones, as you will have to indicate the exact depths that the animal has been found at. The current Values from the Type Depth are only major separations, some covering large depth ranges.

An overview of the Marine Depth Zones will be put on the ANSP web-site shortly.

18. Click OK.

19. Having accessed the Species Valid Name, this should now be ready for publication. You will have to Edit Taxon Name to change the status to Verified. If you have doubts regarding the completeness of the Species Valid Name, do not change the Status.

20. click OK.