The goal of this tool is to allow for explicit and unambiguous reference to ontological concepts within publications, other websites, or applications through the use of Universal Resource Identifiers (URIs). This sounds a little confusing, but the idea is straightforward. Labels used in publications are often not explicitly defined, and when read by others they may be misinterpreted (e.g through synonymy or homonomy). By including in your publication or website a link to a specific ontological concept, for example an anatomical structure, you can state your intention as to how a given word (label/term) is used in your particular paper- "by using the word 'head' I mean the thing that is defined in this manner in this ontology.". Nearly all taxonomic publications, for example, include a statement in their Materials and Methods that indicates where the descriptive terminology in the present work is defined. The analyzer is a powerful tool to aid in the production of these statements. Like with all tools the results of the analyzer should not be published without careful review (see 'Steps to publishing' below). For an example of the analyzer in action see here.
- Cut and paste your text, or type directly into the large text box. Try to limit the text in the box to that pertinent to the underlying ontology being analyzed against.
- Fill out the reCAPTHCA form. If you need help click the small "?" on that form. This is used to prevent spamming or other attacks. Each time you click the submit button you will have to recomplete the CAPTCHA, even after you have successfully filled one out the first time.
- Click Submit and wait (you'll see a little turning spinner).
- Results are displayed in below in a simple table format.
- Download the results by clicking the "Download" button to the right. The downloaded file is a tab delimited file that can be opened directly in a spreadsheet program or other text editor.
- For additional details click on "Detailed breakdown". This will show exactly what text is parsed, where in the text matches were found, a list of synonyms, and a list of homonyms.
- The result table has 4 columns
- The word in the text that matched.
- The concept(s) within the ontology that word is tied to. It is important to note these are NOT identical concepts, in fact each concept is distinctly different is some way, or there is a problem with the ontology.
- The URI. This is the unique link to the concept immediately to its left.
- The reference(s) which use the label in column 1 in the manner of the definition of column 3. Click on a reference to see its full citation.
- The Detailed breakdown will additional aid in interpreting the results of the analysis, it is broken down by:
- Analyzed Text - Use this to confirm that your text was submitted correctly. The analyzer may truncate your text if it is too long, or if it finds other problems.
- Match Map - The words that were matched and returned are highlighted in the context of the text here. Green highlights indicate a 1:1 mapping (i.e. there is only one concept present for the given label. Red highlights indicate that there are multiple concepts for a given term.
- Matched Terms - A simple comma separated list of the terms that were found.
- Matched Classes - A list of the concepts that were matched.
- Homonymous Terms - Of those terms that matched those that are homonyms.
- Synonymous Terms - Of those terms that matched those that are synonyms.
Steps to publishing a "URI Table"
The result table could be formatted for publication, and in the portal.hymao.org example it is particularly useful for Materials and Methods or appendix sections of taxonomic treatise. Here is an outline of the steps you should take (additional functionality is available to those producing descriptions or phylogenetic matrices within mx).
- Generate a result as above.
- Click the download button to download the result. The result is a text file, with column separated by tabs. Use a text editor with many columns to view it, or, alternatively, open excel, and import the file (most versions of excel will *not* import the file correctly simply by clicking on it).
- Carefully review each conceptual match. This is the most important step- do not assume that the result is using the label you have provided in the manner you mean to provide.
- If multiple concepts (definitions) are available for a given label choose the one that you feel matches your concept. Delete the other lines . Repeat for all the labels in the table.
Include the table in the pertinent section of the paper. Include extra columns as needed for notes or comments. It is highly recommend that you pass along your table to the curators of the ontology for them to review, particularly if you have comments or questions.
Providing a printed URI within the text of a publication, for example a taxonomic description, is a first step to modelling the statements we make in publications in a formal manner. There are many other potentially more useful applications of a URI. Including URIs in any form, however, within a publication, will ultimately make the document more interesting to computer-driven indexing of the document. For example all the papers of with the URI referencing the "head of a hymenopteran" could be discovered if each publications about hymenopteran heads included the URI "http://purl.obolibrary.org/obo/HAO_0000397". They could still use the label "head" alone, but a search could differentiate between "head" in the context of hymenopterans, and "head" of, for example, community organizations.
Other sites provide similar services, most notably Bioportal. The functionality within mx allows for a result integrated with other functionality to be returned, and for context specific to mx to be provided.