Overview of "dictionaries" in xDD

Dictionaries in xDD are lists of terms, phrases, and/or regular expressions that are of interest to an individual or that are relevant to a domain of inquiry (e.g., biological taxonomic names, mineral names, genes, proteins). After a dictionary is defined and added to xDD infrastructure, it has several uses, including:

• identifying and grouping documents, document metadata, and xDD-generated data products (e.g., NLP, OCR) that may be relevant to the dictionary
• summarization of counts of terms and number of documents containing terms across the entire xDD document library
• providing additional information content to individual term mentions (e.g., "amphibole" is a "mineral", "PRDX6" is a "protein").

After dictionaries are created on xDD infrastructure, dictionary statistics, summary of counts for terms within dictionaries, and other functionality is automatically made publically available by the xDD REST-ful API. For example, to retrieve basic information about all dictionaries as a JSON object:

https://xdd.wisc.edu/api/dictionaries?all

To retrieve counts of all mentions of terms in a specific dictionary as a JSON object:

https://xdd.wisc.edu/api/dictionaries?dict=minerals&show_terms=true

To retrieve more detailed statistics for counts of terms within a dictionary as a JSON object:

https://geodeepdive.org/api/terms?dictionary=minerals

To retrieve "snippets" of text around individual mentions of a dictionary term as a JSON object, with each mention highlighed using HTML entities:

https://xdd.wisc.edu/api/snippets?term=Abelsonite

(Note that there are default limits on the returned number of documents and snippets within each document. To override these limits and define the number of documents and snippets to return, parameterize the API URL, as described here: https://xdd.wisc.edu/api/snippets).

Defining a dictionary using this repo.

This repository contains an example of one way for an individual to define a github-based dictionary of terms for use within xDD. This approach has the benefit of being: 1. publically accessible to the xDD infrastructure and 2. version controlled.

Two files are required at minimum to define the dictionary:

config.yaml

The configuration for the dictionary. Attributes must include:

name (string) : Name of the dictionary

user (string) : Your preferred email. We will send an email when indexing is complete.

knowledge_domain (string) : General domain of the list of terms provided. For example, a list of taxa may have a domain of biology. A dictionary of elementary particle types may have a domain of physics or particle physics.

case_sensitive (bool) : Whether or not case matters for the terms. If case_sensitive is true, then capitalization of words matters.

word_stemming (bool): Whether or not words should be stemmed before matching is considered. If true, word stemming is applied and the effect is that the matching is looser. For example, "cretaceous" and "cretacallis" both have word stemmings of "cretac". As a general rule, if you want to find proper nouns as terms, word stemming should be false. If you want matching to include variants of a word (pluralizations, verbified nouns, etc), word_stemming should be true.

base_classification (string) : General category or classification of terms contained in dictionary

dictionary.csv

A list of terms in the dictionary, one per line. If multiple words are provided, the first word is treated as the key term, and the others are treated as supplementary terms. This is useful for creating hierarchical/synonym/filter structures.

For example, an entry of:

Homo sapiens,Mammalia,Primates,Hominidae

Will create a dictionary entry of "Homo sapiens", index all documents and mentions of "Home sapiens" in the xDD corpus, and track whether mentions of one of [Mammalia, Primates, Hominidae] are also be mentioned within a document to be considered a match.

Instructions

To create your own dictionary of indexed terms within the xDD infrastructure:

1. Fork this repository into your own repository.
2. Update the config.yaml file with the attributes prescribed above.
3. Update the dictionary.csv file with your list of terms. The first word
   of the line will the primary term matched. The remaining words are
   treated as supplementary terms, and the article is flagged if *any* of
   these additional terms are found. **NOTE** the indexing on the primary
   term will still occur -- the supplemental terms just provide an optional
   level of filtering.
4. Once your changes are complete, send a pull request. This will trigger
   the xDD infrastructure to add your dictionary and begin the
   indexing process.
5. You will get an email when the dictionary is fully indexed.