Data entry tutorial

Introduction

The Paleobiology Database has many data tables and many scripts used to enter and edit data in the tables. In this tutorial you will step through the procedure for entering data into each major table, stopping short right before submitting. If you have any other questions, write to the Database Secretary.

You should read the entire frequently asked questions page before doing anything else. Pay careful attention to the sections "What is the database structure?"; "How is the Database organized?"; "Who can join..."; "How can I form a research group..."; and "Who has access..."

Note: when you log in, be sure to get the "Authorizer" and "Enterer" names right. The authorizer is typically the Ph.D. who is supervising a data entry project; the enterer could be the same as the authorizer, but just as often is a student or postdoc working with the authorizer.

Entering a paper

It's important to enter all the data in every paper, not just the data you need for your specific project. You should proceed in this order:

  1. Enter the full reference.
  2. Enter all taxonomic authority and classification data.
  3. Enter the collection data. Be sure you are not entering duplicates, and split the collections as finely as is reasonable. If you have multiple collections and they are very similar, you may want to use the prefilling option to enter them in rapid succession and then deal with the occurrences later.
  4. Enter the occurrence data.
  5. Reidentify any occurrences in other collections that are discussed in this paper. Remember that a reID of certain material is not the same as a synonymy opinion regarding a name in general.
  6. Add ecological/taphonomic data, if there are any.

What script to use

We store many kinds of data, so there are so many data entry scripts, and it may not be clear which one you should use. Here are some common scenarios.

References

Every major table in the Database is tied back to the references table, which tracks publications yielding assorted data. We record references only if they include some enterable data, and we avoid references (such as review articles) that repeat information from earlier publications. Reference records have a straightforward structure, with author names, publication years, article and journal titles, etc.

  1. From the main menu, hit Add a new reference under "References."
  2. You don't want to enter a duplicate reference, so you must search our data to see if the ref is already there before you continue. Try a very simple search just using the author's last name.
  3. If there are matches, you will get a list. If none of the refs are the same as yours, hit Add reference.
  4. If you got no matches, or if you hit the Add reference button, you will get a data entry form. Fill out every field you can. Don't worry about the project codes if you don't know what they are. If you can, use the "serial's name" pulldown to avoid filling out the "full name" field.
  5. In a real session you would be ready for submission. To avoid saving any test data, hit the Main menu link instead.

Taxonomic data

We have two tables that handle all the basic information of alpha taxonomy. Who named what when (e.g., Linnaeus named Homo in 1758) is recorded in our authorities table (= master name list). The status of a name - either how it should be classified, what it should be synonymized, or why it's flat-out useless - is recorded in our opinions table. We have one short form that feeds into each table.

  1. From the main menu, hit Add/edit taxonomic name under "Taxa."
  2. If you don't have a current reference or want to change it, do a search. Otherwise hit Use current reference.
  3. You now have a simple form that asks you to find a taxon by entering its exact name. This crucial step is needed to make sure that a "new" taxonomic name has not already been entered into the system; or, if you are editing an existing name, to make sure you find it. So, be very careful to enter the name fully and correctly.
  4. If there are one or more existing names spelt like yours, you will be given a list ending with a choice to "create a new taxon record." If you are revising an existing name, choose it based on its author and/or the higher-order taxon that includes it. Otherwise, just select the last radio button.
  5. One way or another, at this stage you will be presented with a taxonomic authority data entry form. Carefully consult the taxonomy data entry FAQ before you fill in any of the fields.
  6. Click Main menu if you want to discard the test data.
  7. Once you have entered or revised the authority data, you can classify or synonymize the taxon using the taxonomic opinion form. Hit Add/edit taxonomic opinion under "Taxa" and then follow the equivalent of steps 3 - 6.

Collections

We separate information about where fossils are found into two tables that have different data entry forms: one for contextual data about collections and another for occurrences within collections.

The collections form records geography, stratigraphy, lithology, taphonomy, collection methods, etc. Each collection is supposed to represent the most geographically and stratigraphically restricted unit you can identify, and ultimately would correspond to the fossils collection from one bed in one spot by one worker in one field season.

Before you enter any data, you should read the collection and occurrence data entry tip sheet in its entirety.

  1. From the main menu, hit Add a new collection under "Collections."
  2. You must have a "current reference" to enter any data. The Database gives you a chance to select one whenever you start the data entry process. Because this is just a demonstration, you should pick any arbitrary ref; if you were really entering data, you would have to be careful to get the right one. So, fill in the "Author's last name" with something common like Johnson and hit Search.
  3. Click on the radio button next to one of the references and hit Select reference.
  4. You don't want to enter a duplicate collection, so you must search to see if similar collections have been entered. Try a very broad but meaningful search of the collections table. Examples: fill in one short word from the "Collection name" only; fill in "County" only; fill in one word from the "Formation" name only. Do NOT search by "Authorizer" or "Enterer."
  5. You should get back a list of similar collections. Make sure none of them are the same as the one you are trying to create. It helps to click on the collection names, look at the full records on the resulting pages, and then hit the back button to get back to the list.
  6. If you did not find any matching collections, or if you hit Add a new collection, you will get a data entry form. Fill out every field you can following the instructions on the collection and occurrence data entry tip sheet.
  7. Click Main menu if you want to discard the test data.

Occurrences

The "occurrences" comprise the taxonomic list for a collection, plus abundance data, comments, etc. You can't create occurrences unless you have (or someone has) already created the corresponding collection. You may add new occurrences to an existing list entered by someone else under a different authorizer's name.

  1. From the main menu, hit Add/edit occurrences for a collection under "Occurrences."
  2. If you don't have a current reference or want to change it, do a search. Otherwise hit Use current reference.
  3. To see the occurrences, you need to find the collection they belong do. Enter some broad and meaningful search terms and hit Search collections.
  4. The search should return a list of collections. Click the highlighted collection number to the left of the collection that you want.
  5. You can now modify old occurrences and/or create new ones by typing in names below the old records. Note that the genus/higher taxon and species/sp./indet. fields are required. If your authorizer doesn't own the old records, they won't be writeable.
  6. Click Main menu if you want to discard the test data.

Reidentifications

If a newer paper says that the identification in an older taxonomic list is wrong even though the name itself is valid, you need to record the new ID or "reidentification." Note that you should not change the occurrence itself; instead, we want to know what name originally was used (the occurrence) and what name now should be used (the reidentification).

  1. From the main menu, hit Reidentify occurrences under "Occurrences."
  2. If you don't have a current reference or want to change it, do a search. Otherwise hit Use current reference.
  3. You now have a collection search form that can be used in two ways. First, you might want all occurrences in one collection. Most of the fields can be used for this kind of a search. Hit Search collections when you have entered the right search terms for that collection.
  4. As with the occurrence search, you will be given a list of collections. Click the highlighted number of the collection you want.
  5. Second, you might want multiple occurrences of the same taxon, not necessarily from just one collection. Fill out the field for taxonomic names and no other fields, and then hit Search collections.
  6. Either way, at this point you should have a list of occurrences with original identifications printed at top and lines with input fields for reidentifications. Fill out only the reidentifications you need to, ignoring the others. If the first page doesn't have the occurrences you need to correct, hit the View next 10 occurrences link to navigate forwards.
  7. Click Main menu if you want to discard the test data.

Reclassifications

Our system normally figures out for you which taxonomic authority record (= formally listed name) goes with which occurrence or reidentification. However, sometimes there are two names that mean different things (i.e., apply to different authority records), but are spelt the same way. The typical reason is that one name is for a plant and the other is for an animal. In those cases, you need to tell the system which authority goes with your occurrence.

  1. From the main menu, hit Reclassify occurrences under "Occurrences."
  2. You now have a regular collection search form. Hit Search collections when you have entered some useful search terms.
  3. As with the occurrence search, you will be given a list of collections. Click the highlighted number of the collection you want.
  4. You will be given a form that can have either or both of two sections. First, there may be a section that gives the "Classification" of the taxa in the collection. Select the appropriate authority data in the pulldown menus for the taxa you need to reclassify, ignoring the others. Second, there may be a "Taxa that cannot be classified" section. You can't do anything about those names unless you first create the taxonomic authority record that goes with the name (see below).
  5. Click Main menu if you want to discard the test data.

Ecological/taphonomic information

The Database can record general information about higher or lower taxa such as their skeletal composition or diet. The information can be useful if (say) you want to download your occurrences with each one having a dietary category based on its taxonomic identity. Any data you enter for a taxon (e.g., a family) also will be applied to its lower taxa (e.g., its genera), unless those taxa have been scored directly themselves using this function. So, once you enter the family you don't have to enter the genera, unless they're different.

  1. From the main menu, hit Add ecological/taphonomic information under "Taxa."
  2. If you don't have a current reference you'll need to search for one and select it.
  3. On the next page, select a taxon by entering its exact name. If you enter a taxon whose name is not in the authorities table, you will be kicked back to this page. If you know the taxon's name is correctly spelt but you still can't get past the page, you probably need to create a taxonomic authority record first (see above).
  4. You will be presented with an ecology/taphonomy data entry form. Carefully consult the ecology/taphonomy data entry tip sheet before you fill in any of the fields.
  5. Click Main menu if you want to discard the test data.