GNames
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
- 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
-
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
-
GNmatcher
Refer to the GNmatcher documentation for its installation.
-
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 localhost: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
License
The GNames
code is released under MIT license.