Please select from the following to navigate through the manual. You may also refer to the forum page to troubleshoot or report any problems, or contact us at firstname.lastname@example.org.
-2.1 Selecting existing nodes
-2.2 ITIS nodes
-2.3 Non ITIS nodes
3. Node information
4. Assigning citations to node information
5. Add a Citation
6. Interaction information
-6.1 Add an Interaction
-6.2 Add an observation of an interaction
7. Database schema (pdf)
There are three forms of information that the interface is set up to have enter:
(i) Node information (e.g., a taxon’s body-size, mobility, etc.)
(ii) Interaction information (e.g., taxon 1 preys on taxon 2)
(iii) Citations (to be associated with each datum that is entered)
The following manual is arranged accordingly.
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The database refers to “nodes” rather than “species” because nodes need not be species- specific taxa; they may be higher level taxonomic groups (e.g., Rhodophyta (red algae)) or aggregated assemblages of indistinguishable taxa (e.g., “Phytoplankton”) (Note: we will often use the terms “species”, “taxon” and “node” interchangeably in this manual, since most nodes will actually be specific species.)
Information regarding a taxon should be entered using the highest taxonomic resolution available in the source citation you will be referencing. That is, while species-specific information is the most desired, you may also enter information for a node that represents a genus, or a family, etc., or an assemblage of indistinguishable species.
In order to enter information on the interactions between the stages of two nodes, both nodes (and the relevant stage of each node) must already be present in the database. Therefore, the first screen that you will come to after logging-in is the “Node Search” page. You can also reach this page using the “Add, Edit Nodes” tab in the top banner.
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SELECT EXISTING NODES
Our database makes use of the Integrated Taxonomic Information System (ITIS) database. This should minimize errors associated with relic synonyms and misspelled taxon names. However, the ITIS database is not complete; many taxa found along the eastern Pacific are absent. Our database stores these taxa separately, identifying them using a “working name” until the time that they are entered into ITIS.
To determine whether a node has already been entered into our database, you can either:
1. Look for and select it from the list of already entered nodes using via “List Nodes/Interactions” tab at the top of the page, or
2. Search for it using the “Node Search” fields. For the latter, it is best to start typing the scientific name of the taxa into the “ITIS latin name” field. The interface will start checking the ITIS database for existing entries as soon as you start typing, and will return a drop down list of all names that match
When you have found and selected a taxon from this list, one of two things will happen:
1. If the taxon is not already present in our database, the ITIS ID and ITIS common names fields will be updated, but nothing else will happen. You will have to Add New Node (see “Adding ITIS Nodes”below).
2. If the taxon is already present in our database, the other ITIS fields will be updated and a new page will open up below enabling you to enter information for the node (see “Entering Node & Stage Information” below).
If you cannot find the taxon in the ITIS database, search for it in the “Working name” field using either its scientific (latin) name or common name. If you cannot find the taxon using any of the search fields, look for it in the list of previously entered taxa accessible via the “List Nodes/Interactions” tab at the top of the page. If you still cannot find it, you will have to create a new non-ITIS node (see “Adding Non-ITIS Nodes” below).
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ADDING ITS NODES
If you have found a taxon in the ITIS database that is not already present in our database, you will have to add it as a new node using the “Add New Node” button which will appear once you have selected the ITIS taxon. A new screen will open (see figure to the right) requesting additional information regarding the taxon you have selected.
The working name should represent an easily recognizable synonym for the node. Most often, this will be the common name (e.g. Latin name: Enhydra lutris, Working name: Sea otter).. Check “is assemblage” if the taxon is not a formal species (e.g., phytoplankton).
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ADDING NON ITS NODES
Create a new node if the taxon that you are looking for is not found using either the ITIS or “Working name” search fields and it is not present in the list of entered taxa. To do this, use the “Add Non-ITIS Node” tab at the top of the page.
Each non-ITIS ID must point to a valid ITIS ID at some higher (parent) taxonomic level. If your new node’s parent is already in ITIS, this will be a simple three-step process: (1) Use the “Parent Search” field to search the ITIS database for the scientific name of the most specific taxonomic name you can identify your new node to (2) Enter the taxonomic level and the Latin name of your new node. (3) Specify a representative “working name” for the node, and fill in the rest of the requested information.
If you have multiple taxonomic levels that are not already in ITIS, you will need to repeat the above steps several times, starting with the level of the parent that is already in ITIS. From there, work your way down by using the “Parent Search” field to search for the either an ITIS node or non-ITIS node that represents the next parent. For example, if you wanted to enter a new node for the genus Enhydra whose taxonomic hierarchy is …>Mammalia>Carnivora>Mustelidae>Lutrinae>Enhydra, but Lutrinae did not exist in the ITIS database, then you would have to first add a node for Lutrinae with the parent Mustelidae before adding the node for Enhydra with the parent Lutrinae.
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ENTERING NODE AND STAGE INFORMATION
As soon as you have selected a node that already exists in our database a new page will open below to enable you to enter information for the node and its stages (see image below). The page is split into two sections. The top section is for information that is relevant to the entire node, the bottom is for information that is stage-specific. Our database distinguishes between four different animal life-stages (adult, juvenile, larval, egg) and two algal life-stages (sporophyte, gametophyte). The default “stage” is to be used when stage-specific information is not available (i.e. when the source citation doesn’t specify the life-stage of the taxon), or when the specified life-stage is not among the provided options.
Note: Mousing-over an entry field will cause an explanation to pop-up describing what kind of information is to be entered.
Note: Information that has previously been entered into the database is shown to the right of each entry field. You can delete any entries which you have entered yourself (under your username).
There are two basic ways to enter data:
1. If you are entering information from a single source into multiple different fields, then it will be easiest to fill in all the fields for which you have data before pressing the “Set Values” button at the bottom of the Node or Stage sections of the page. A new screen will then pop-up requesting you to enter the citation information for the reference (see Assigning Citation below) .
Note: When you are planning to enter multiple pieces of information from a single citation it may be convenient to add the citation to the database first. Select the “Add Citation” tab at the top of the screen to do so.
2. If you are entering data into only a single field, or are entering information from multiple sources for a single node or stage, then it will be quickest to hit the Return key on your keyboard after each value that you’ve entered. Pressing the Return key will cause the citation pop-up screen to appear.
Note: Make sure that you are entering data in the current units. Mouse-over the entry field to see which units are required. A link to Wolfram alpha’s unit conversion website is provided at the top of the Stages section.
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When you hit the return key or press the “Set Values” buttons, a pop-up screen will appear instructing you to select the citation to associate with the data you have entered.
To do so, you can either: (1) select from among the most recently used citations using the “Citation” drop-down list, (2) search for an author’s name to see if your citation has previously been entered, or (3) add a new citation to the database. This will open a new pop-up screen (see Adding Citations & Authors). You will automatically be returned to the previous screen once you have added the new citation.
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ADDING CITATIONS AND AUTHORS
You can add new citations either by selecting the “Add Citation” tab at the top of the screen, or by selecting the “Add New Citation” link when assigning a citation to entered data.
First, insert all authors and co-authors of your citation (in the order they appear in the citation). Each (co)author gets entered separately. Only after all authors have been entered into the database should the other information for the citation be entered and then saved. (Do not add all co-authors together as one “author”.)
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ENTERING INTERACTION INFORMATION
You can add information regarding the interaction between two nodes or their stages either by selecting the “Add, Edit Interactions” tab at the top of the page, or by selecting a previously entered interaction using the “List Nodes/Interactions” tab.
Our database keeps track of the presence and information regarding the interaction between the stages of two nodes by recording source-specific observations of the interaction. The interaction between Sea otters and California mussels, for example, can have multiple observations associated with it, each from a different citation. It is thus necessary to establish the presence of an interaction between the stages of two nodes before one is able to add a citation-associated observation of it.
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Search for the two nodes in the provided search fields. Each node’s General stage will be selected by default. If you are entering stage-specific information, select the appropriate stage from each node’s drop-down menu.
Note: If a stage is not available in the drop-down menu, you will have to close the “Node Interaction” screen and establish the stage’s existence by adding the desired stage on the “Node/Stage Information” page.
If you have selected a previously entered interaction from the “List Nodes/Interactions” tab, then the page will be populated automatically. Lists will appear below each selected node summarizing all the interactions that have previously been entered for it.
If an interaction has already been established between two nodes/stages, a third list will appear between the selected pair of nodes (below the “Interaction Type” drop-down menu) summarizing all the observations of this interaction that have already been entered into the data base.
If the presence of an interaction between two selected nodes/stages has not previously been established, then the space below the “Interaction Type” drop-down list will be empty. Select the type of interaction you want to establish (trophic, competition, facilitation, or parasitic) and press the “Add Interaction” button.
Note: You can delete any observations which you have entered yourself (under your username). However, because of the way the database is set up, it is also possible for you to remove (i.e. delete) any interactions established by others. Therefore, be VERY careful when doing using the “remove interaction” button!!!
Note: Be sure to add an observation of an interaction after you have added a new interaction. Adding an interaction between two nodes/stages does not save information regarding its existence to the database. Information will only be saved when an observation is added.
Note: Be sure to enter observations for all the interactions that a citation provides, even if observations for an interaction from a different citation have already been entered into the database.
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ADD OBSERVATION OF INTERACTION
You can add observations of an interaction between two nodes/stages (once its presence has been established). After ensuring that you have the correct type of interaction selected from the drop-down list (trophic, competition, facilitation, or parasitic), press the “Add Observation” button. This will open up a new window that will differ slightly between the different types of interactions.
Associate a citation to the observation, either by selecting it from the drop-down list of recently used citations, or by searching for one of the citation’s authors.
A citation is all that is necessary for adding an observation to the database. However, if the citation provides any of the information requested in the entry fields, this should also be entered.
Note: If a single citation provides multiple different types of observations for a given interaction (e.g., field observations and laboratory experiments), these should be entered as two separate observations.