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Instructions to editors

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You have access to edit all the information in the system only within the taxonomic group assigned to you as an associate editor. Before you change existing information, it is important that you do not "overwrite" valuable information. For example, a common misspelling of a name can be valuable to be kept in the database. In that case, it is better that you create a new entry and link the misspelling to the correct name. Below you will find a list and a short explanation of what is possible in this system. If you have any questions, please do not hesitate to ask the system admins by clicking here .

What information do we prioritize?

MinimalClassification, Species name, Authority and publication date
Highly desiredBasionym, Original publication reference, Holotype information (type locality, museum, number, ...)
Optionaladditional synonyms, references, images, morphological description, specimens, distribution, feeding type, weblinks

Instructions

Frequently asked questions

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How to log in

Please ask the data manager for a password if you should not yet have received one. The access rights are linked to the higher taxa in the classification tree. In other words, you will only be able to edit information in your particular taxon group.

If you have a separate web interface (e.g. http://www.marinespecies.org/copepoda) then always log in via this website, so that all the data you entered/edited is automatically part of this collection. Go to [My Aphia] to check your edit rights and change your password if needed.

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Quality indicators

Images, specimens, vernaculars, notes, distributions, taxa, … carry quality indicator icons.

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Edit taxon details

If you want to change the details of a taxon that already exists in WoRMS, you search the taxon and click on [edit taxon]. You can change all the information except the AphiaID.

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Add a new accepted taxon

If you do a search for a taxon and do not find it, then you can add it. Every name in WoRMS is linked to a "parent" taxon: e.g. a species epithon is linked to its genus or subgenus, a genus is linked to its family or subfamily. Search for the parent taxon using the search tool and click on [add child taxon]. This will open a new window "Aphia add a taxon", with an empty taxon form. Fill in all the necessary information and click on [add]. The fields indicated with a red asterisk are mandatory fields. The information in the parent field cannot be changed, as you indicated that you wanted to create a "child" taxon for the taxon you started from. The record status of the name will automatically be "checked by editor" and in the edit history at the bottom of the page, the "date", and created by "your name" will be listed. When adding the authority make sure you use author(s), year and brackets () and/or accents if needed. Mark the environment (marine/brackish/freshwater/terrestrial) if you create a new taxon.

See also: How can I add a subspecies when the species name on itself is not in use?

See also: Can I add taxa that are in press?

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Add a new unaccepted taxon

In WoRMS invalid (unaccepted) synonyms are linked to valid (accepted) taxa. This requirement is not needed for cases like:

  • nomen nudum: i.e. a name that does not comply with the name requirements of the codes, such as lack of a description or diagnoses or reference to a description or diagnosis or a type specimen is lacking for publications after 1999
  • nomen dubium: i.e. a name of uncertain application, because it is not possible to establish the taxon to which it should be referred. A good example is the "Ascothoracida" genus Laocoon. There is a debate whether this is based on a parasite or on a detached piece of the host. It is clearly a dubious name
  • temporary name: e.g. to create higher rank taxa to accomodate child taxa for which the classification is not sorted yet
  • species inquirenda: i.e. an incompletely defined species that requires further characterization, it is impossible to identify the species
  • Incertae sedis: of an uncertain seat; i.e. of uncertain taxonomic position; or when the original material has not been studied or the description is insufficient. Usually applied to family and generic names
More information about name statuses can be found at Hawksworth, D.L. 2010. Terms Used in Bionomenclature. The naming of organisms (and plant communities). Copenhagen: Global Biodiversity Information Facility, 216 pp

Go to the parent taxon and follow the same procedure as for adding a new valid taxon (click on [add child taxon]). Now change the status into "unaccepted" and enter the "accepted name", this is a drop-down list. If the accepted name is not found, then add it first. If possible fill in all other information and click on [add].

See also: Can I link an unaccepted name to more than one taxon?

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Add a new environment flag

You should add an environment flag (to indicate if marine taxa) while adding a taxon or if the name is already created you need to go to the taxon page and click on [edit taxon]. There are four environment flags (marine, brackish, freshwater and terrestrial). Each flag has three options (Yes, No and Unknown). As a default, WoRMS shows only marine and/or brackish water species based on the environment flags: marine = Yes or Unknown and/or brackish = Yes or Unknown. It is especially important that pure freshwater and terrestrial species are ruled out by saying No at the marine and brackish environment.

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Add a new source

In WoRMS, all the information e.g. taxon, distribution, notes, etc... should as much as possible be linked to a source (which can be a publication reference, a database or an expert person). The sources are managed separately in the WoRMS literature module. You can only link to a source if the source is available in the database. Before you add a source, please check if the source is not yet in the database. Go to literature and click on [add source]. It is also possible to add a weblink (e.g. DOI) and to upload the full text publication. The maximum file size is set at 100 MB. If you would like to add many sources, upload a larger file or if you would experience any problems during the uploading, please contact us.

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Link a source to a taxon

To link a new source, go to the taxon details page. Before you link a source to a taxon you have to see if it isn’t already linked.

Click on [link source]. This will open a new window "Aphia link a source to a taxon", with an empty form. Enter the first letters of the first authors’ last name and click on [pick]. This will open a new window "Aphia pick list: source", where you can select your source from the drop-down list and click on [pick]. Fill in the Use and Pagnr. and click on [link source]. If this is for a new species, then pick the correct source, change 'Use' to original description and add the pages that the species was described on.

You can also search for an author that is not first author by using the wildcard % and last name to find anywhere in the author string. You can select the "remember" button, so that the reference automatically appears the next time you want to link a source to a taxon (helps a lot if you enter many names of a single publication). The system is set so that the accent marks used in author names will not hamper the search (e.g. if you type in Gomez you will get Gómez or Mollmann will get Möllmann).

You can add multiple sources if needed. Say you want to record all the authors that published on the taxa, then you create a new link for each source as needed. And then change the 'Use' to one of the 14 choices (original description, basis of record, additional source, source of synonymy, redescription, new combination reference, status source, toxicology source, taxonomy source, ecology source, identification resource, subsequent type designation, misapplication or context source) as necessary.

Source "use" values:

  • Original description: publication in which the present taxon was originally described (under its basionym)
  • Basis of record: source consulted when entering the present record
  • Additional source: source that contains additional information about the present taxon
  • Source of synonymy: source that contains information on the synonymized taxa
  • Redescription: source in which the present taxon is redescribed in a modern way
  • New combination reference: source in which the present combination was first proposed
  • Status source: source that contains information on the current status of the present taxon
  • Toxicology source: source that contains information on the toxic nature of the present taxon
  • Taxonomy source: source that contains information about the classification of the present taxon
  • Ecology source: source that gives information about the relations and interactions between the present taxon and its environment, including other organisms
  • Identification resource: source that contains information on the identification of the present taxon
  • Subsequent type designation: publication in which the type-species or –specimen of the present taxon was designated
  • Misapplication: source in which the present taxon name was used in an erroneous way
  • Context source: source used to link a taxon to a subcollection of WoRMS

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Add a new vernacular

You can add common names of species and higher taxa in as many languages as possible. One scientific name can have more than one name in a foreign language, or one vernacular name can be linked to several scientific names. You can add a note and link to a source to provide more information.

See also: Can we emphasize preferred vernacular names?

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Add a geographical location

Go to the Marine Regions Gazetteer, login with your WoRMS password and go to [My Marine Gazetteer].

It is possible that the location is not listed in the drop-down list in WoRMS, but is present in the gazetteer. First search if the location is available in the gazetteer (via the search tool), before you start adding a new location record. If the location is present in the gazetteer, then click on [add to aphia] and the location is added to the drop-down list in WoRMS.

If the location is also not present in the gazetteer, than click on the add buttons to add a geographical location, source or place type (find the buttons on [My Marine Gazetteer]). Fill in the necessary fields and click on [create]. A link to the parent location will create the hierarchical tree of the localities. For marine locations (such as lagoons, bays, sandbanks, etc… use the country name + Exclusive Economic Zone (or the sea/marine area it belongs to) as its parent, instead of the country name, which refers to the land part. The geographical location is automatically transferred to WoRMS.

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Add a distribution record

Go to the taxon page and click on [add distribution]. This will open a new window "Aphia add distribution record". Fill in all the fields and click on [add]. Pick the geographical location as detailed as possible from the pick-list. If the place name is not in the list, add it first (see above). Don't enter e.g. "Oostende, Belgium", but only enter "Oostende". Use the country name Exclusive Economic Zone if it is a marine species, rather than just the country name. The geographical names are linked to the Marine Regions gazetteer, which hierarchically structures the geo-names.

There are 3 possibilities for the status of a distributiun record:

  • Valid: the record is certainly valid
  • Doubtful: doubts on whether the species really lives there
  • Inaccurate: taxon was cited for this area but it is clear that it does not live there (misidentification, wrong label, etc)
You can add the reason and source for doubtful or inaccurate distributions.

Latitude and Longitude are only needed for point locations. In this case the geo-unit will be a general place name (e.g. seas, countries, ...). You can choose between the decimal or DMS (Degrees, Minutes, Seconds) format, click on DMS to switch. For decimals, don't forget to use the minus sign for South and West. For example 40S = -40. The date should be the begin date. The end date can only be filled in if the observation was only made during a certain period. Note that you can enter the type locality either via the specimen module or as a distribution (flagging on "type locality"). If the type locality is entered in the specimen module, then there is no need to enter it again as a distribution record (because this is something we can create automatically). Some explanation of the various flags linked to distribution records:

  • Type locality: the locality of the holotype
  • Vagrant: species appeared accidentally outside its natural range
  • Specimen: this record represents a specimen deposited in a museum
  • Map: derived from indication on a map of the place where the species was found

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Add many distribution records more easily

When you have a species list of a single location or a list of geographical locations of a single species, then it is much easier to enter these distribution records using the "rapid distribution entry" page. Go to the [My Aphia] screen and click on "Rapid Distribution Entry". You can ask the system to remember the taxon or the geographical location for the next entries. This saves you time because you don't need to select these items over and over again. Also the source and other information that you add to the fields is automatically remembered by the system.

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Add a new specimen

Go to the taxon page and click on [add specimen]. This will open a new window "Aphia add specimen record" with an empty specimen form. Fill in all the fields. The taxon name is filled in automatically. This module is also used to add type localities. You can add as many attribute notes (e.g. ecology, morphology, habitat etc...) as required. An attribute can also be a URL link to an online specimen record (add attr. "URL", and the full URL in the next field).

See also: When adding a specimen, should I use the original species name or the currently accepted?

You can add multiple identifications to specimens (previous misidentifications of specimens): add the specimen details, subsequently click on [edit] and change the status to invalid, and then add a new identification.

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Add a feeding type to a taxon

This is where you can add info about the taxon, how and where it feeds. Go to the taxon page and click on [add feeding type]. This will open a new window "Aphia add feedingtype". Select a feeding type from the predefined drop-down list, add more information if possible and click on [add]. There is also a drop-down list ‘Stage’: if this feeding type only occurs in a certain life stage of the taxon you can indicate this here. You can add a feeding type for every life stage if necessary. You can also add host information for parasites and symbionts. There is a drop down pick list to find the host. There is a note field to add information such as where on the host it lives (e.g. collected from nasal cavity or attached to gills, etc…). If WoRMS does not find a match in the host name, then it means it is not in the database and has to be added. Contact info@marinespecies.org here , let them know and they will have the host taxon name added.

Possible feeding types:

  • Carnivore: flesh-eating organism
  • Deposit feeder: feed on organic material contained in the soft sediments of the sea bottom. Sometimes called ‘bottom-feeder’
  • Deposit feeder: non-selective: eats any kind of deposits
  • Deposit feeder: selective: prefers a certain type or size of particles
  • Deposit feeder: subsurface: exploit food located deeper in the sediment (few cm)
  • Deposit feeder: surface: feed on particles on the surface
  • Detritus feeder: animals that consume decomposing particulate organic matter (as opposed to dissolved organic matter)
  • Epigrowth feeder: eating from the top layer of plant and algae growth
  • Filter feeder: organism that feeds on particles of organic matter that are suspended in water by creating a water current
  • Grazer: feeds on plants and algae by scraping along a surface
  • Herbivore: plant eating organism
  • Interface grazer: eating from the middle layer of plant and algae growth
  • Not feeding: doesn’t eat
  • Omnivore: all-eater or polyphage, eats plants, animals, algae, fungi, …
  • Parasite: an organism that grows, feeds, and is sheltered on or in a different organism while contributing nothing to the survival of its host
  • Parasitic: ectoparasitic: shelters on the host
  • Parasitic: endocommensal: commensalism is an interspecific, symbiotic relationship in which two different species are associated, wherein one is benefited and the other neither benefited nor harmed. Here the beneficial organism lives in the other organism
  • Parasitic: endoparasitic: shelters in the host
  • Predator: an organism that preys on other animals as a source of food
  • Predator/omnivore: an organism that actively searches for food but eats everything
  • Scavenger: organism that feeds on dead animal material, and sometimes also drift algae
  • Suspension feeder: organism that feeds on particles of organic matter that are suspended in water
  • Suspension feeder: facultative: organism that can choose between suspension feeding or another type of feeding
  • Symbiotic: epizoic: Epizoic mean that one organism is living on the surface of another organism. The relation is beneficial for at least one member
  • Symbiotic: unspecified type: a close, prolonged association between two or more different organisms of different species that may, but does not necessarily, benefit each member
  • Unknown

Possible life stages:

  • Egg: animal develops in the female gamete
  • Juvenile: not fully grown or developed
  • Adult: fully grown or developed, mature
  • Larva: the newly hatched, earliest stage of any of various animals that undergo metamorphosis, differing markedly in form and appearance from the adult
  • Postlarva: 1. Stage in the development of a bony fish between the resorption of the yolk sac and the appearance of juvenile characteristics. 2. The larval stage following the nauplius stage in Crustacea, many crustacean groups have a distinct name for this stage
  • Spat: an oyster or similar bivalve mollusk in the larval stage, especially when it settles to the bottom and begins to develop a shell
  • Subadult: an individual that has passed through the juvenile period but not yet attained typical adult characteristics
  • Zoea: a larval form of crabs and other decapod crustaceans, characterized by one or more spines on the carapace and rudimentary limbs on the abdomen and thorax
  • Nauplius: the free-swimming first stage of the larva of certain crustaceans, having an unsegmented body with three pairs of appendages and a single median eye
  • Polyp: a coelenterate, such as a hydra or coral, having a cylindrical body and an oral opening usually surrounded by tentacles
  • Medusa: one of the two forms in which a coelenterate exists. It has a jelly-like umbrella-shaped body, is free swimming and produces gametes
  • Ephyra: a stage in the development of discophorous medusae, when they first begin to swim about after being detached from the strobila
  • Megalopa: post larva of crustaceans, follows on the zoea
  • Planula: free swimming, flattened, ciliated, bilaterally symmetric larval form of various cnidarians, forms from the fertilized egg of a medusa or from a polyp

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Add a link to a taxon

Go to the taxon page and click on [add link]. This will open a new window "Aphia add a link". You can enter a url, add a text (this will appear on the website) and click on [add].

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Add a PDF to a taxon

Go to the taxon page and click on [add link]. This will open a new window "Aphia add a link". Click on "upload PDF" and choose a file from your machine. You can add a text explaining the document, for example species diagnosis, original description etc... (this will appear on the website) and click on [add].

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Add a note (characteristic) to a taxon

Go to the taxon page and click on [add note]. This will open a new window "Aphia add a note". You can add free text (in any language), select the type of the note and click on [add].

Notes are arranged in three types:

  • Checked/added by taxonomic editor or information retrieved through a WoRMS global species database
  • Added by a thematic editor (thematic species databases) (=trusted information)
  • Coming from another source (=unreviewed information)

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Add an image to a taxon

Go to the taxon page and click on [add image]. This will open a new window "Aphia add image". The taxon name and your contact details are automatically filled in. You can further describe the image, select the image from your computer and click on [upload]. Unless you indicate otherwise in the description field, the Creative Commons Licence is our default, which means the pictures can be used for non-commercial purposes and with proper credits to the author. The maximum file size for upload is set at 100 MB.

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Add an image to a specimen

After you have created the specimen record, go to the species page and click on [add image] next to the specimen record. This will open a new window "Aphia add image". The taxon name, specimen name, and your contact details are automatically filled in. You can further describe the image, select the image from your computer and click on [upload]. By pressing [show all] you can see all types of existing specimens, so you can add images to all types. Unless you indicate otherwise in the description field, the Creative Commons Licence is our default, which means the pictures can be used for non-commercial purposes and with proper credits to the author. The maximum file size for upload is set at 100 MB.

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Change a taxon name

Go to the taxon page and click on the [edit taxon] button just next to the name. Change the information and click on [update].

See also: How can I update the classification?

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Change the status of a name

Go to the taxon page and click on [edit taxon]. Change the status into "unaccepted" or any other possible status from the pick list and in case it is a synonym, enter the "accepted name". If possible fill in all other information, for example the unaccept reason and click on [update]. If you change the status of a name, it doesn't mean that the status of its children is changed.

Possible statuses for a name:

  • Accepted: the used name is accepted in the present literature
  • Unaccepted: The used name is NOT accepted in the present literature
  • Nomen nudum: a name that does not comply with the name requirements of the codes, such as lack of a description or diagnoses or reference to a description or diagnosis or a type specimen is lacking for publications after 1999
  • Alternate representation: to link species that are represented twice: once with and once without subgenus. Alternate representation can also be used for a species and its nominal subspecies (note: you can only add a subspecies if the species is present in the database). See example in the box below
  • Nomen dubium: a name of uncertain application, because it is not possible to establish the taxon to which it should be referred. A good example is the "Ascothoracida" genus Laocoon. There is a debate whether this is based on a parasite or on a detached piece of the host. It is clearly a dubious name
  • Temporary name: to create higher rank taxa to accomodate child taxa for which the classification is not sorted yet
  • Taxon inquirenda: an incompletely defined taxon that requires further characterization, it is impossible to identify the taxon

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Change the record status

Each record status carries a quality indicator:

When you have changed taxonomic information of a taxon, the record status will automatically be set to "checked: verified by taxonomic editor", represented by the green v-sign. The edit history will include "date" and "changed" by "your name".

When no changes are required you can validate the taxon by clicking on the quality indicator pictogram, the record status will be set to "checked: verified by taxonomic editor".

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Change (the status of) a distribution

Go to the taxon details page and click on [edit] next to the distribution record. There is a drop down list with 3 possibilities:

  • Valid: the record is certainly valid
  • Doubtful: doubts on whether the species really lives there
  • Inaccurate: taxon was cited for this area but it is clear that it does not live there (misidentification, wrong label, etc)

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Change collection information for a specimen

Go to the taxon details page and click on [edit] next to the specimen record. This will open a new window "Aphia edit specimen details". Edit the information as needed and click on [update].

If a specimen description has been published, but afterwards turns out to be given the wrong name, you can create a trace of its identification history. Go to the taxon page and click on [details] or [edit] next to the specimen record and click on [add identification]. Do not forget to edit the previous identification by flagging-off the valid button.

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Change a source

When a source is linked to a taxon, and you click on [edit] source on that taxon page, you can change the use of that source for that particular taxon. For example change "original description" to "redescription".

If however you want to correct the source, e.g. the spelling of the reference, you have to go to the source details in the literature module, and subsequently click on [edit source]. The changes are automatically reflected throughout the entire database.

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Remove information from the database

In principle we do not delete information which has been published in primary literature or which is in common use (e.g. many hits in google). In that case you need to correct the error by changing the status (see Edit taxon details).

Sometimes, information can be wrongly entered into the database or spelling mistakes were made. Sometimes entries into the database are based on published spelling mistakes, but the name never got in common use. This kind of information should be removed as soon as possible before they start their own life by either correcting the alternate representation or deletion.

To remove information from the database, you need to click on the respective [delete] buttons. An email is sent to the database management team, who can finally delete the record. When this is done they will inform you via email.

Note that each record has a unique aphia ID number. The ID numbers of the deleted items are never overwritten. The reason of the deletion of a record is archived. This is important for other data systems that are linked to these records.

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Frequently asked questions

How come there is a difference between WoRMS and some of the subcollections like Isopoda etc ?

It is important to understand that all the information in WoRMS is in a single database (so each name has a single instance!), but on the basis of contexts (compare it with keywords), we can make collections or sections in WoRMS and display it on different web interfaces. For Editors, the context option is available near the bottom of each edit form. If you add new information to WoRMS and you don’t want to be bothered flagging on the context to each new item, then login via your own section website (same login) and your context is automatically added to every new record.

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How can I know what species of my taxon are in WoRMS, but are not part of my collection?

Go to the search tool, and select your taxon in the box "Limit to taxa belonging to" and select your collection context in the "Exclude context" box. You can further choose the status from a drop-down list and you can limit the search to non checked taxa or taxa that are in quarantine by flagging off the right box. You can also specify environment, taxon rank, etc …

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How do I know what species have been added or changed by my co-editor?

Go to the search tool, and select the action (all, created, changed or checked), indicate the person and if necessary select a begin date. You can further set other items such as limit to species rank, limit to a particular family or valid names only, etc...

For information added in the last week see the Weekly Digest

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How can I update the classification?

Go to the taxon details page and click on [edit taxon]. Change the parent by selecting it from the drop-down list. All the children are automatically moved as well.

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How can I add a subspecies when the species name on itself is not in use?

You can only add a subspecies if the parent species is present in the database. Use the status "alternate representation" for the species and link it to its nominal subspecies in case the species name is not used separately.

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Can I link an unaccepted name to more than one taxon?

It often happens that a higher taxon became invalid and its children are spread over many other taxa. When you know what the type taxon is, then the accepted taxon is the new parent of the type taxon. The problem is of course when you don't know what the type taxon is. In that case you have to contact the data management team here and ask to change the status without linking to an accepted taxon. You always have to add the reason of the invalid status.

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How do I enter an occurrence record in a paper that mentions the original paper, which also used a synonym name?

The ideal solution would be to have the possibility to link a single distribution record to more than one name and source. But the system is not built to cope with this so we suggest you enter the information as it was published in the paper that you are encoding, but that you add a note citing the original reference and original name.

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What should I do if not all genera can be assigned to a subfamily for example?

If for example there is a taxon (any rank) that doesn't fit anywhere in the current classification, you must create a temporary parent with the name "X incertae sedis", where X is the name of the first following parent.

Some people would like to skip the sub or super or infra ranks in the classification. We leave this decision up to the editor.

See examples at: http://www.marinespecies.org/aphia.php?p=taxlist&tName=%incertae%20sedis.

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Can we emphasize preferred vernacular names?

Yes this is possible. When adding/editing a vernacular name you can tick the "preferred" box. However, trying to settle on a single "correct" common name is tricky. Developing a complex thesaurus of common names falls more within the scope of an ethnographic or linguistic project. In many cases the vernacular names come from the older literature and we should also record these in WoRMS for the benefit of people working with that old material.

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Can I add taxa that are in press?

In principle we do not add taxa to WoRMS that have not been formally published according to the different Codes. Only if your paper is in press, so not before submission and only after acceptance, you may add the taxa to WoRMS or change the status of taxa. But always clearly refer to the source by linking to the reference of your paper. This also counts for synonyms. If you think the species is a synonym, but you have not published it, you can add a note like this: "The validity of this recently described species needs to be re-evaluated".

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Can you explain how the citation on each page works?

In the same way as citing regular publications we would like to encourage citing data that have been published online. When a taxon name has been created, changed or marked as checked by an editor, he or she will automatically become the (co)author of that webpage. The citation has the format as a chapter in a book: [author(s)] [Year]. [chapter] in [Book]. [Publisher]. [Page]

=> Editors (Year). Taxon + Authority. In: GSD title. Accessed through the World Register of Marine Species at URL on [date].

When the taxon has not yet been verified by an expert, WoRMS is listed as the author. A member of the data management team is not considered an expert of the taxon and therefore will not receive "the authority" for a webpage.

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When adding a specimen, should I use the original species name or the currently accepted?

It is better to add the specimen details to the original species name. So you don't loose information, and it is easier to trace back the specimen in the museum collection. Besides, because the taxon name is linked to the currently accepted name, the information on the specimen is also shown on the webpage of accepted taxon.

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How are we dealing with the correct citation of the year of publication of a new species´ description when the online version and the printed version appear in different years?

When you cite the publication containing the original description, you cite it with the date of the print edition, but also include the date of the online edition in the original description reference, so people can see that there is no oversight from the part of the WoRMS editor.

For example: Neopycnodonte zibrowii Gofas, Salas & Taviani in Wisshak, Lopez Correa, Gofas, Salas, Taviani, Jakobsen & Freiwald, 2009
The source says: Deep Sea Research I 56(3): 374-404 [published online 29 October 2008; printed copies deposited by January 2, 2009, in several museum libraries as stated in acknowledgements; printed edition of the journal dated March 2009].

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How should I handle taxa that were originally introduced with a question mark: e.g. "?Bifrontia zanclaea"?

Art. 5.3 "A typographical sign such as ? [...], when used to qualify the application of a scientific name, does not form part of the name of a taxon [...]. So, you just drop the question mark.

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How should I handle species that currently are *tentatively* placed in synonymy (the kind of thing that is usually preceded by a "?" in synonymies)?

Flag them as synonyms, and under "unaccepted reason" write "uncertain synonym".