Registering for the LD KB
Welcome to the LDKB (https://ldfknowledgebase.com) You do not need to register to browse or search the site. However, if you wish to contribute to the forum, registration is required. To register, click on the “Create an account” at the top right of the main page (shown in the red box in the image below):
You will be directed to a form page where you can enter your professional and contact details (see below).
The account creation form page requires that you enter a username as well as a display name, however these do not need to be different. Your username is what you will use to sign in to the site, while the display name is what other users will see if they read entries that you have contributed.
Institutional and locational information that you provide will not be shared, however we require this information to ensure that you are a member of the life detection science community (at this time, we are not accepting users who do not have professional science or engineering institutional affiliations).
Once you have completed the registration form, click “Register” in the lower right of the form. A pop-up will inform you that you have successfully registered and are awaiting confirmation.
An email will be sent to the address you provided, and you can then confirm your registration through the link in the email (which looks like the image below).
After clicking this link to activate your account, you can then set your password.
Once your password has been set, your registration will be successful and will await full approval from the administrators of the site. Once you have registered and been approved, you will be able to sign in to the LD KB using the “Login” option at the top right of the Home page. When you are logged in, you will see “Welcome, [your name]” at the top right of the page while using the site.
Welcome to the LDKB!
Browsing and Searching on the LDKB
The LDKB has several ways for users to browse or search the available information. (Note: You do not need to register or be logged in to search or browse the LDKB, but must be logged in to contribute comments or entry materials. If you do not have an account, see the above section for more information on registering).
On all the pages of the website, there is a menu bar on the top. Shown below for the Home page, this menu bar has both a search text box (outlined in red) at the top left, and a ‘Browse’ tab (outlined in yellow).
Clicking on the ‘Browse’ tab will lead to the top-level structure of the knowledge base. The same happens upon clicking ‘ENTER’ on the middle of the Home page.
Navigation while browsing or searching
From any page in the LDKB, you may always conduct a new search in the search text box at the top. The ‘Home’ tab in the menu bar will take you back to the Home page while the ‘Browse’ button will take you to the top-level structure of the knowledge base, as explained below.
The navigation bar also includes links to the “About” and “Help” sections of the website, as well as a contact option. When browsing through the structure of the site, the contact option provided is to “Email Contact”. This will send an email to the administrators of the website. When viewing specific potential biosignatures, arguments, and evidence, the option presented is to “Email Curator”. This will send an email to the curator for the specific feature that you are exploring.
Browsing the LDKB
Once you have clicked ‘ENTER’ from the Home page or clicked on the ‘Browse’ tab within the navigation bar at the top of any page, you will be taken to the top level structure of the knowledge base (shown below). This structure begins with the categories of Chemistry, Structure and Activity.
From this top-level page of the knowledge base, a user can find background information about any of the three categories. To do so, click on “Background” within the category’s field. This will bring up the background information. Longer background texts can be expanded (by clicking on ‘[read more]’ within the text box). Also, the option of downloading background information as a .txt file has been provided (click on the ‘Download background’ box within any background section to download the information).
From the top-level of categories, a user can browse the content within the site by clicking on any one of the category titles. This will cause a branching tree to open up below the category (as shown below for Chemistry). Just below the level of categories are topics from within those categories that have been identified by the life detection science community in previous CLD-hosted workshops and beta-phase content development activity rounds as being the primary topics/observables for measurement relevant to life detection within the corresponding category.
The topics (also referred to as measurement parameters) within each category are presented within boxes that have the same coloration as their categories, while below each topic is a list of potential biosignatures within the given topic. As the website continues to grow, these lists will evolve and expand. Some potential biosignatures appear in olive/grey text when they do not yet have published arguments and supporting evidence on the site. Potential biosignatures which do have published information appear in black text.
On any topic page within the tree, you can click on the open checkbox above the title of the topic to select or deselect all of the potential biosignatures within that topic. Likewise, you can click on open boxes to the left of any potential biosignature to highlight them and add them to a list for further filtering.
Below is a zoomed-in image of the “Abundance Distribution of Compounds” and “Enantiomer Ratios” topics within the Chemistry category. The checkbox for abundance distribution has been checked, highlighting all of the potential biosignatures in that list, while only “amino acids” has been highlighted for enantiomer ratios.
From these topic pages, you can build a list of topics and potential biosignatures that you would like to browse.
Once you are finished with your selections of topics and potential biosignatures, you can click the blue “Go” button at the bottom of the page to display them. Alternatively, you can select the red “Clear” button to reset all selections (as shown below).
In the example below, we have selected the “Amino Acids” potential biosignature from the topic of “Abundance Distribution of Compounds” and then clicked “Go.” This has taken us to a new window of “Selected biosignatures” where we can view a filterable list of any potential biosignatures we have selected.
At this point, you have the option to refine your selections by using radio buttons to filter by specific environments. In general, the “All” environments option is automatically selected when the list first appears. However, should you be interested in filtering your list of selections by environment, you can click on one or more of the environment options. Please note: the current options were selected by members of the life detection community as having the highest value in this sortable list. Should you wish to request a new environment or a change to this list, you can use the “Email Contact” tab to make the request and site administrators will ensure that your request is shared with the Center for Life Detection for further consideration.
From your filtered list of selected potential biosignatures, you can now view each potential biosignature along with the background information provided by the curators and contributors. Longer background sections within each potential biosignature box can be expanded if needed, and background sections can be downloaded as .txt files as well for off-line reading.
Each potential biosignature box has the option to “View” a potential biosignature’s content (the blue button) or to “Remove from list”, which will remove the selected potential biosignature from the filtered list.
At the very bottom of the “Selected biosignatures” page are the options “Add/Change biosignatures”, “Back to filters”, and “Exit”. The “Add/Change biosignatures” button will return you to the top-level structure of the knowledge base to select or deselect more topics and potential biosignatures to add to your list. Clicking on “Back to filters” will simply take you to the top of the “Selected biosignatures” page, while clicking “Exit” will return you to the Home page.
Viewing a Specific Biosignature
After clicking “View” on any biosignature from the “Selected biosignatures” list, you will be taken to the page for that potential biosignature (see example below).
At the top of this page is the title of the potential biosignature within a box (colored to match the category it came from). You will once again see the background text with the option of expanding the background (by clicking on the “Background” button - this also presents the option of downloading the background information again).
Within the box containing the background is also the information about the date when the entry was created, the date of its most recent update, and the name of the curator for that entry. A registered user will be able to click on the name of the curator to open a contact page where users can send direct messages to the curators. Furthermore, users can access the “Comment” option within the background text box in order to provide comments or ask questions about the potential biosignature and the background information provided (you must be logged in to provide comments or send messages).
Below the text box at the top containing the background information for the potential biosignature in question, you will find the evidence-supported arguments, separated by key criteria that were identified by the first cohort of content developers from diverse subfields of the life detection science community.
As described in the Glossary in the “About” section of the site, the two main criteria used on the site are Prevalence and Feature Strength. For each of these, there are biological and abiotic arguments. Due to this, the sections that are immediately visible on the knowledge base under the text box are “Biological Prevalence”, “Biological Feature Strength”, “Abiotic Prevalence”, and “Abiotic Feature Strength”.
For each of these main criteria boxes, you can hover your mouse over the name of any criterion that is underlined with a black squiggly line and it will reveal a general definition for the criterion as applied across the entirety of the Knowledge Base.
Within the criteria box you will also see a button labeled “Definition”. This will open a pop-up text box with further information about the criterion as it applies to the biosignature in question. Further information is provided by the curators where they feel it is appropriate and/or necessary. If the pop-up text box is empty, it means that a curator has not provided extra definition information for the criterion in question.
Also within the criterion box, the number of arguments (both pro and con) that have been contributed will be presented within parentheses following the title of the criterion.
In order to view the arguments that are available within a given criterion, you must click on the criterion box, which will cause a drop-down feature to open. For instance, in the example below, “Biological Feature Strength” has been clicked, expanding that criterion for further viewing of available arguments.
The knowledge base is structured such that pro and con arguments can be provided with regard to any of the criteria. Pro arguments/evidence (always presented on the left-hand side of the page) are those that support the specific definition for that biosignature criterion, while the Con arguments and evidence (presented on the right-hand side) are those that directly counter a Pro argument. In some cases, it can be difficult to determine the difference between a Con argument for something biological and a Pro argument for something abiotic (and vice versa); in such cases, curators for each biosignature will make the final determination of how to structure the arguments.
When browsing the LDKB (on a desktop browser version of the site), you will notice that some arguments are linked and will appear within the same section separated by a horizontal black line. This shows that the arguments are specifically related to one another. Often this will just be one pro and con argument that oppose one another, but can include several pro or con arguments that are linked together. On a mobile or tablet device, this feature will not be apparent.
Each argument is presented within its own text box, along with options to view the relevant environments (as determined by the contributor and curator) by clicking on “Environments”, to view the available evidence provided by users by clicking on the “Evidence” button (which also includes in parentheses the number of pieces of evidence), and for users to provide comments and questions by clicking on the “Comment” button.
While Prevalence and Feature Strength are the primary criteria, there are several other criteria, as defined in the Glossary of the About section. Within Prevalence, there are General prevalence arguments as well as Congruence prevalence arguments (where congruence represents the degree to which the attributes of a particular feature or its inferred source are consistent with its occurrence in a specific environment). Similarly, within Feature Strength there are General feature strength arguments as well as those that are delineated by the criteria Production, Survivability, and Patchiness.
Within the argument text boxes, just after the title of the argument, the further refinement of the criteria will be shown in brackets.
Upon clicking on the gray “Evidence” button within the argument text box, the box itself will be expanded to show the evidence entries (see below). Each piece of evidence that supports an argument is derived directly from the scientific literature.
You can click on the yellow circle with an “e” or even on the text of the evidence entry itself to bring up a new window showing the information about the evidence and the supporting literature.
This window (see below) shows a short description of the evidence and a brief summary (both provided by the knowledge base contributor) as well as the authors, abstract, and citation information for the article or book from which the evidence is supported. There are several citation formats available, and the option to download the BibTeX or Endnote version of the citation is also available. Clicking on the blue chain link beside the title of the evidence will allow you to access the piece of literature online (NOTE: THIS FEATURE IS COMING SOON).
Searching the LDKB
From any page on the website, you can access the Search bar at the top left of the page.
In the example below, we have entered the search term “lipids.” Clicking the “GO” button will then allow us to search this term.
The search result (below) has come back with two categories, “Fatty Acids” and “Lipids.”
Selecting the “Fatty Acids” result will then take us to the expansion of that topic, as we had done for “Amino Acids” while browsing earlier.
Here, again, we find the actual arguments and evidence that exist for the biosignature of interest, broken down into the main feature categories. From this point, you can explore the arguments and evidence just as you can as was shown above while browsing.
Contributing Evidence and Arguments to the Knowledge Base
Beyond providing comments and emailing curators and admin, registered users can also contribute arguments and evidence to the website.
For adding new lines of evidence to specific arguments that already exist on the site, click on the “Add Evidence” button within the field of the argument (outlined in red below). Make sure you are logged in to your Knowledge Base account.
Once you have clicked on “Add evidence”, it will open a new window (see below).
All of the fields in red boxes above will need to be filled in order to add new lines of evidence. There are some key features that the user must be aware of in adding new evidence.
First, on the left-hand side of this window, the user must provide a short description/title for the evidence as well as a longer description. The title must be shorter than 250 characters, but must be sufficient to explain briefly how the evidence applies to the argument. The longer description should be more than a simple evaluation or synopsis of the piece of literature that will be cited, but should rather be a thorough explanation of which piece of evidence or set of data from the accompanying cited literature justifies the support for the argument in question. For instance, one piece of literature may provide multiple pieces of evidence that support the arguments. There may even be some pieces of literature that support both Pro and Con arguments within the same criterion or which provide evidence for both biological and abiotic factors with regard to a specific feature. Any questions regarding the nature of evidence and what constitutes a sufficient explanation should be sent to the curators and/or admin for the site.
Please note: the evidence title and explanation are NOT the same thing as the title and abstract of the article. Appropriate additions of evidence should include a title that briefly describes the exact piece of evidence in question, and the description should inform a reader more thoroughly of what the supporting evidence says.
Beyond adding an evidence title and explanation, the user must also provide the relevant citation to the literature. There are several ways to do this, including adding a citation from BibTeX or Endnote code, adding a citation manually, and/or searching for a citation from PubMed or Google Scholar.
To add evidence via BibTex or Endnote, click on either “Import BibTeX” or “Import Endnote” at the top of the evidence addition window. Import BibTeX allows the user to import a .bib file or to paste the relevant code for upload while Import Endnote allows the user to upload a .enl file from Endnote.
Adding evidence manually requires filling in the required fields. Please be careful and ensure that the citation is appropriately entered (citations will be reviewed by curators as well as other users and a contributor may be asked to correct issues if a citation is not entered correctly). When adding evidence manually, you can select whether you are entering a journal or a book entry. Please note that a volume number is required for journals while a chapter number is required for books (if there are no volume or chapter numbers available, you may use an “X” to fulfill this requirement).
Searching for citations is currently supported for PubMed and Google Scholar reference databases. Once you have selected “Search”, you will be given the option of which database to search within. PubMed supports searching by field (i.e. title, author, year, etc.), while searching within Google Scholar is done by keyword only. Once you have clicked “Search” after filling in the text field, you will receive a list of relevant citations that match your search. Once you find the correct citation, click on it, and it will populate the citation fields.
Please note: not all citations will entirely populate the necessary fields. For instance, many returns from Google Scholar will be missing a volume number or DOI. In those cases, you must find the citation and enter the missing information. We also request that you include the abstracts for journal articles when available. This might require you to copy-and-paste the necessary information from the article directly.
Once you have sufficiently filled in the required fields, you can click on “Submit Draft”. This will notify the curator that new information has been drafted and is ready for their review. A user can view any pieces of evidence they have contributed, even if unpublished. This will allow you to edit your contribution, if needed, even before a curator has reviewed the entry. The example below shows a piece of evidence that is awaiting review. The red bar that says “Waiting for approval” will disappear once a curator has reviewed and approved of a new evidence entry.
In the above image, there are two new buttons to the left of the evidence entry. The button in grey with an image of a pen over paper allows the user to edit the entry. (A user can only edit their own entries). The red button with an image of a trash can is for deleting that entry.
Once your evidence entry has been approved by a curator, it will be made visible to all other users of the site. If a curator does not approve of an entry, they will send you an email requesting necessary changes or informing you of the reasons for which the entry cannot be published on the website.
New arguments and counter-arguments can be provided within the main criteria for any potential biosignature. Arguments should be well-thought and well-structured statements that can be supported by one or more pieces of evidence from the literature.
New Pro and Con arguments can be added by clicking on the relevant buttons within a specific criterion region (outlined in yellow below).
By clicking on the text for “Add argument”, a pop-up window will appear allowing for a new argument to be created.
The pop-up window will feature a text field where the language of the argument should be written. The argument should be concise and yet structured enough to be explanatory for other users. Below the text field, the user can determine whether the argument applies to all available environments or whether one or more specific environments are more pertinent. Also, the user must determine whether an argument is a general prevalence or feature strength argument or whether further refinement through other criteria is necessary. If adding an argument to the prevalence section, the options will include “General” and “Congruence”, while adding a feature strength argument will allow for the options of “General”, “Production”, “Survivability”, or “Patchiness”. (See the Glossary for further information on these criteria.)
Each new argument must include at least one line of supporting evidence in order for it to be reviewed and then published. Once you have added your argument, you will be able to edit it or delete it (just as with adding evidence), but you must add at least one line of evidence before you will have your new argument reviewed by a curator.
One other way to add arguments, specifically to add counter arguments to a Pro or to a Con argument, is to click on the words “Add counter” at the bottom of any argument text box. This will allow you to add an argument that will automatically be linked to the argument that you are countering.
What is the difference between argument and evidence?
For the purpose of LDKB, arguments and evidence can be defined as follows: Argument is a statement aimed at persuading others that a given hypothesis is true (or false). Evidence is a fact or information that supports an argument. While argument is just a statement, evidence provides description of concrete scientific results that allow us to propose that this statement is true.
How do I assess whether my argument is properly formulated?
A properly formulated argument:
- clearly refers to biological/abiotic pro or con,
- does not contain jargon or undefined terms, so it is understood to non-experts,
- has support in evidence from scientific literature,
- does not duplicate arguments that already exist in LDKB.
How do I assess if my evidence is properly formulated?
In a properly formulated evidence:
- it is clear how it supports the argument,
- there is no jargon or undefined terms, so it is understood to non-experts,
- the source (scientific paper) is faithfully represented,
- without excessive details it is clear what was done and what were the results,
- no information that is not relevant to the argument is given.
It is not recommended to copy the abstract as evidence description, as it rarely satisfies these criteria.
Can I enter an argument without evidence?
Can I enter argument(s) pro without providing argument(s) con or vice versa?
Yes, you can, but LDKB will be richer if both pro and con arguments were provided if available.
What is the difference between argument con and counterargument?
Counterargument relates directly to the argument. For example, an abiotic pro argument for enantiomeric excess might be “In some meteorites, there is large excess of L-amino acids”. A counterargument would be “These meteorites are rare, special cases”. To enter counterargument to a given argument click on “add counter” button. Arguments con do not have to be related to argument pro.
Can I have multiple counterarguments for a given argument?
Yes, you can.
What is the difference between “biological con” and “abiotic pro”?
For feature X, biological con arguments address statements: (a) X is not required for life (prevalence), and (b) even if X is produced by life, it would be unlikely or impossible to find it, e.g., because it is destroyed much faster than produced or because it is altered to become indistinguishable from X produced abiotically (feature strength). Any arguments related to abiotic sources of X are not biological con.
Abiotic pro arguments address a statement: X can be produced abiotically (prevalence) and it should be possible to find it (feature strength).
Biological con and abiotic pro describe, respectively, false negatives and false positives. These two types of errors are distinct and should be assessed separately.
Can I have multiple pieces of evidence for a single argument?
Yes. In fact, it is highly desirable to have multiple pieces of evidence for an argument if only available.
Several papers contain similar evidence related to a given argument; how do I deal with this?
Each piece of evidence has to be entered separately, even if it is similar to the one that already exists. Multiple references to a single piece of evidence are not allowed.
One paper contains evidence for several arguments; how do I deal with this?
Each evidence should be formulated separately and entered to support the appropriate argument. It is OK to use the same reference several times in LDKB if needed.
My argument/evidence is applicable only to a specific subset of the listed environments; what should I do to include this information?
The best approach is to formulate your argument or evidence such that it includes this information. If specific information about the environment applies to evidence, it can be included in the description of the evidence (the left side of the evidence template) and added to keywords (the right side of the evidence template) for easy search.
I believe that a piece of evidence in the literature is incorrect; should it be excluded from the KB?
No. Content providers are not charged with evaluating evidence, which means that all relevant evidence should be included. However, any objections should be noted as comments.
Can I add a new potential biosignature?
No. However, users can propose new potential biosignatures to the administrator. They have to be approved by the potential biosignature taxonomy group and the administrator.
Why my argument/evidence is not visible to all?
Every new argument or evidence has to be reviewed and approved by the curator. Only then it is published and becomes visible. It may take a few days.