Example:

Organic Chemistry:
  - Medicinal Chemistry
  - Polymer Chemistry:
      - Plastic Materials
      - Carbon Nanomaterials:
          - Carbon Nanotubes
          - Graphene
  - Petrochemistry
Inorganic Chemistry:
  - Coordination Chemistry
  - Organometallic Chemistry

Usage: dents <command> <operator> <arguments>

DENTS commands use inverse function mapping - one to many, not many to one. This is chosen so the first argument of one type can have many arguments (that are of a different type than the first and are all of a similar type) after it

process

Takes a YAML file and turns it into a .lent file

• Usage: dents process file.yaml
• no additional operators or arguments

tagtofiles

filetotags

filter

0. Terminology and stylistic choices
   • Some set theory will be used in combination with colloquial English because it is the best way to communicate some things clearly and unambigoiusly
   • Hex-line: refers to a standard 16-byte row in a hex dump
   • Metadata: is a common term meaning “data about the data” used here.
   • Ipsodata: contrasted with metadata. “Data that is the data itself”. Commonly used English terms for “the data itself” such as {“core data”, “primary data”, “source data”, “raw data”} do not capture what I want to mean here, the data itself which is opposed to the data-about-the-data. And so the Latin root “ipso”, meaning “itself”, is used as a prefix to “data”.
     
   • Offset: When offset is said here, I am referring to only the length of the offset and not the content of the offset.
1. Over-arching design choices for DENTS
   • DENTS is made for a nested tagging system for tree tag hiearchies. Each tag has a parent (except for the top level tags) and can have children.
   • DENTS is designed for a multi-user session many simultaneous query database
   • The file format is designed for human-readability in hex dump
   • No existing solutions accomplish any of these points
2. DENTS is designed for quick lookup for children tags for a multi-user-session database. This means hash table lookup (O(1) complexity) as opposed to tree traversal or linear traversal (O(N) complexity).
3. File Header (32 Bytes, or 2 hex-lines)
   1. DENTS magic number in unicode
   2. Version number
   3. Tags quantity denoter
4. Tags Metadata (4a)
   1. Tags Metadata = {Tag metadata individual length indicator, Tag meta/ipsodata individual offset indicator, Tag name}

DENTS uses a custom binary implementation, which is difficult to extend or write queries for. So after DENTS, I will make LENTS, (Local Extendable Nested Tagging System), which will likely be a wrapper around Refsplitr and PartiQL/DynamoDB Local, which allows for more customizable queries. LENTS will probably retain the same command schema as DENTS.

• Refsplitr - “refsplitr is a package designed to assist researchers dealing with bibliometric data by providing tools for author name disambiguation, author georeferencing, and coauthorship network mapping using data from the Web of Science”¹
  • Author disambiguation
  • Support for multiple authors per file
  • Author/Institution timeline mapping
  • Institution disambiguation
• PartiQL - “An expressive, SQL-compatible query language giving access to relational, semi-structured, and nested data.”²
  • allows for more custom queries, including queries with the additional information above
• Potential Implementations: Metadata Extraction Tools
  • ExifTool by Phil Harvey - “ExifTool is a platform-independent Perl library plus a command-line application for reading, writing and editing meta information in a wide variety of files.”
  • Apache Tika - “The Apache Tika™ toolkit detects and extracts metadata and text from over a thousand different file types (such as PPT, XLS, and PDF). All of these file types can be parsed through a single interface, making Tika useful for search engine indexing, content analysis, translation, and much more.”
• Visualization tools