gnames

README

GNames

• RESTful API Documentation
• RESTful API Example

The goal of the GNames project is to provide an accurate and fast verification of scientific names in unlimited quantities. The verification should be fast (at least 1000 names per second) and include exact and fuzzy matching of input strings to scientific names aggregated from a large number of data-sources.

In case if you do not need exact records of matched names from data-sources, and just want to know if a name-string is known, you can use GNmatcher instead of this project. The GNmatcher is significantly faster and has simpler output.

• Features
• Installation
  • Installation prerequesites
  • Installation process
• Configuration
• Usage as API
• Usage with GNverifier
• Web-Logs
• Known limitations of the verification
• Development
• Authors
• License

Features

• Fast verification of unlimited number of scientific names.
• Multiple levels of verification:
  • Exact matching (exact string match for viruses, exact canonical form match for Plantae, Fungi, Bacteria, and Animalia).
  • Fuzzy matching detects human and/or Optical Character Recognition (OCR) errors without producing large number of false positives. To avoid false positives uninomial names only checked for exact match.
  • PartialExact matching happens when a match for the full name-string is not found. In such cases middle or end words are removed and each variant is verified. Matches of names with the last word intact does have a preference.
  • PartialFuzzy matching is provided for partial matches of species and infraspecies. To avoid false positives uninomials only checked for exact match.
  • Virus matching provides viruses verification.
  • FacetedSearch allows to use flexible query language for searching.
• Providing names information from data-sources that contain a particular name.
  • Returning the "best" result. The BestResult is calculated by a scoring algorithm.
  • Optionally, limiting results to data-sources that are important to a GNames user.
• Providing outlink URLs to some data-sources websites to show the original record of a name.
• Providing meta-information about aggregated data-sources.

Installation

Most of the users do not need to install GNames and can use remote GNames API service at http://verifier.globalnames.org/api/v1 or use a command line client GNverifier. Nevertheless, it is possible to install a local copy of the service.

Installation prerequesites

• A Linux-based operating system.
• At least 32GB of memory.
• At least 50GB of a free disk space.
• Fast Internet connection during installation. After installation GNames can operate without remote connection.
• PostgreSQL database.

Installation process

1. PostgreSQL

   We are not covering basics of PostgreSQL administration here. There are many tutorials and resources for Linux-based operating systems that can help.

   Create a database named gnames. Download the gnames database dump. Restore the database with:

   gunzip -c gnames_latest.tar.gz |pg_restore -d gnames
   

2. GNmatcher

   Refer to the GNmatcher documentation for its installation.

3. GNames

   Download the latest release of GNames, unpack it and place somewhere in the PATH.

   Run gnames -V. It will show you the version of GNames and also generate $HOME/.config/gnames.yaml configuration file.

   Edit $HOME/.config/gnames.yaml according to your preferences.

   Try it by running

   gnames rest -p 8888
   

   To load service automatically you can create systemctl configuration for the service, if your system supports systemctl.

   Alternatively you can use docker image to run GNames. You will need to create a file with corresponding environment variables that are described in the .env.example file.

   docker pull gnames/gnames:latest
   docker run -env_file path_to_env_file -d -i -t -p 8888:8888 \
     gnames/gnames:latest rest -p 8888
   

   We provide an example of environment file. Environment variables override configuration file settings.

Configuration

Configuration settings can either be given in the config file located at $HOME/.config/gnames.yaml, or by setting the following environment variables:

Env. Var.	Configuration
GN_CACHE_DIR	CacheDir
GN_JOBS_NUM	JobsNum
GN_MATCHER_URL	MatcherURL
GN_MAX_EDIT_DIST	MaxEditDist
GN_PG_DB	PgDB
GN_PG_HOST	PgHost
GN_PG_PASS	PgPass
GN_PG_PORT	PgPort
GN_PG_USER	PgUser
GN_PORT	Port
GN_WEB_LOGS_NSQD_TCP	WebLogsNsqdTCP
GN_WITH_WEB_LOGS	WithWebLogs

The meaning of configuration settings are provided in the default gnames.yaml.

Usage as API

Please note, that currently developed API (documentation) is publically served at https://verifier.globalnames.org/api/v1.

If you installed GNames locally and want to run its API, run:

gnames rest
# to change from default 8888 port
gnames rest -p 8787

Refer to GNames' RESTful API Documentation about interacting with GNames API.

Usage with GNverifier

GNverifier is a command line client for GNames backend. It uses publically available remote API of GNames. Install and use it according to the GNverifier documentation.

GNverifier also provides web-based user interface to GNames. To launch it use something like:

gnverifier -p 8777

Web-Logs

By default, Logs are not shown. To enable the service logs change WithWebLogs to true in the configuration file.

To aggregate logs with an NSQ messaging service, provide an address for TCP service of nsqd, for example 0.0.0.0:4150 by changing WebLogsNsqdTCP in configuration file, or GN_WEB_LOGS_NSQD_TCP.

Known limitations of the verification

• Exact matches of misspellings that might exist in poorly curated databases prevent to find fuzzy matches from better curated sources.

  To increase performance we stop any further tries if a name matched
  successfully. This prevents fuzzy-matching if a misspelled name is found
  somewhere. It is helpful to check 'curation' field of returned result,
  and see how many data-sources do contain the name.
  

• Fuzzy matching of a name where genus string is broken by a space.

  For example, we cannot match 'Abro stola triplasia' to 'Abrostola triplasia'. There is only 1 edit distance between the strings, however we stem specific epithets, so in reality we fuzzy-match 'Abro stol triplas' to 'Abrostola triplas'. That means now we have edit distance 2 which is usually beyond our threshold.

Development

• Install Go language for your Linux operating system.
• Create PostgreSQL database as described in installation.
• Clone the GNames code.
• Clone the GNmatcher and set it up for development.
• Install docker and docker compose.
• Go to your local gnames directory
  • Run make dc
  • Run docker-compose up
  • In another terminal window run go test ./...

Authors

• Dmitry Mozzherin

License

The GNames code is released under MIT license.

Documentation

Overview

Copyright © 2020 Dmitry Mozzherin <dmozzherin@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.