Ghini’s goals and highlights¶
Should you use this software? This question is for you to answer. We trust that if you manage a botanic collection, you will find Ghini overly useful and we hope that this page will convince you about it.
This page shows how Ghini makes software meet the needs of a botanic garden.
If you already know, and all you want is to do something practical, check our user-contributed recipes.
According to the Wikipedia, »A botanic(al) garden is a garden dedicated to the collection, cultivation and display of a wide range of plants labelled with their botanical names«, and still according to the Wikipedia, »a garden is a planned space, usually outdoors, set aside for the display, cultivation, and enjoyment of plants and other forms of nature.«
So we have in a botanic garden both the physical space, the garden, as its dynamic, the activities to which the garden is dedicated, activities which makes us call the garden a botanic garden.
Botanic Garden Software¶
At the other end of our reasoning we have the application program Ghini, and again quoting the Wikipedia, »an application program is a computer program designed to perform a group of coordinated functions, tasks, or activities for the benefit of the user«, or, in short, »designed to help people perform an activity«.
Data and algorithms within Ghini have been designed to represent the physical space and the dynamic of a botanic garden.
In the above figure, a simplified view on the database, the highlighted blocks are those relative to objects you definitely need insert in the database.
We distinguish three main sections in the database. Start reading the graph from the right hand side, with the relevant Taxonomy information, then step to administering your Collection, and finally consider the physical Garden.
The central element in Ghini’s point of view is the
its links to other database objects lets us better understand the structure:
Accession links Planting to Species
Accessionrepresents the action of receiving this specific plant material in the garden. As such,
Accessionis an abstract concept, it links physical living
Plantings—groups of plants placed each at a
Locationin the garden— to the corresponding
Species. It is not the same as an acquisition from a source, because in a single acquisition you can access material of more than one species. In other words: a single aquisition can embark multiple accessions. An
Accessionhas zero or more
Plantingsassociated to it (0..n), and it is at all times connected to exactly 1
Plantingbelongs to exactly one
Speciesmay have multiple
Accessionsrelating to it.
Accessionstays in the database even if all of its
Plantingshave been removed, sold, or have died. Identifying the
Accessionconsistently connects all its
Accession at the base of the history of your plants
Contactsprovide plant material for the garden; this information is optional and smaller collectors might prefer to leave this aside. A
Propagationtrial may be unsuccessful, most of the time it will result in exactly one accession, but it may also produce slightly different taxa, so the database allows for zero or more
Propagation(0..n). Also a
Contactmay provide zero or more
Accession and Verification opinions
Specialists may formulate their opinion about the
Speciesto which an
Accessionbelongs, by providing a
Verification, signing it, and stating the applicable level of confidence.
Accessing your own Propagations
Accessionwas obtained in the garden nursery from a successful
Accessionand all of its
Plantingsto a single parent
Planting, the seed or the vegetative parent.
Even after the above explanation, new users generally still ask why they
need pass through an
Accession screen while all they want is to insert a
Plant in the collection, and again: what is this “accession” thing
anyway? Most discussions on the net don’t make the concept any clearer.
One of our users gave an example which I’m glad to include in Ghini’s
the above three cases translate into several short usage stories:
- activate the menu Insert → Accession, verify the existence and
correctness of the
SpeciesHeliconia longa, specify the initial quantity of the
Accession; add its
Plantingat the desired
Plantingto correct the amount of living plants — repeat this as often as necessary.
Plantingto split it at separate
Locations— this produces a different
Plantingunder the same
Plantingto add a (seed)
Plantingto update the status of the
- activate the menu Insert → Accession to associate an accession to a
Propagationtrial; add the
Plantingat the desired
In particular the ability to split a
Planting at several different
Locations and to keep all uniformly associated to one
the possibility to keep information about
Plantings that have been
removed from the collection, help justify the presence of the
People using Ghini only sporadically may prefer ignoring the database structure and look at it as two nested sequences of objects, each element of the sequence being necessary to add element at the next level.
In order to get down to an Accession, you will need four levels, as in this example:
A quite complete set of Families and Genera are inserted in your database at the moment Ghini initializes it. So all you need is adding Species and Accessions, in this order.
When placing a physical Plant (relative to an Accession) somewhere in the garden, you need to describe this “somewhere” digitally, as a Location in the garden.
not-so-brief list of highlights, meant to whet your appetite.
When you first start Ghini, and connect to a database, Ghini will initialize the database not only with all tables it needs to run, but it will also populate the taxon tables for ranks family and genus, using the data from the “RBG Kew’s Family and Genera list from Vascular Plant Families and Genera compiled by R. K. Brummitt and published by the Royal Botanic Gardens, Kew in 1992”. In 2015 we have reviewed the data regarding the Orchidaceae, using “Tropicos, botanical information system at the Missouri Botanical Garden - www.tropicos.org” as a source.
Ghini will let you import any data you put in an intermediate json format. What you import will complete what you already have in the database. If you need help, you can ask some Ghini professional to help you transform your data into Ghini’s intermediate json format.
Ghini will allow you define synonyms for species, genera, families. Also this information can be represented in its intermediate json format and be imported in an existing Ghini database.
Ghini implements the concept of ‘accession’, intermediate between physical plant (or a group thereof) and abstract taxon. Each accession can associate the same plants to different taxa, if two taxonomists do not agree on the identification: each taxonomist can have their say and do not need overwrite each other’s work. All verifications can be found back in the database, with timestamp and signature.
helps off-line identification¶
Ghini allows you associate pictures to physical plants, this can help recognize the plant in case a sticker is lost, or help taxonomic identification if a taxonomist is not available at all times.
exports and reports¶
Ghini will let you export a report in whatever textual format you need. It uses a powerful templating engine named ‘mako’, which will allow you export the data in a selection to whatever format you need. Once installed, a couple of examples are available in the mako subdirectory.
annotate your info¶
You can associate notes to plants, accessions, species, …. Notes can be categorized and used in searches or reports.
garden or herbarium¶
Management of plant locations.
All changes in the database is stored in the database, as history log. All changes are ‘signed’ and time-stamped. Ghini makes it easy to retrieve the list of all changes in the last working day or week, or in any specific period in the past.
simple and powerful search¶
Ghini allows you search the database using simple keywords, e.g.: the name of the location or a genus name, or you can write more complex queries, which do not reach the complexity of SQL but allow you a decent level of detail localizing your data.
Ghini is not a database management system, so it does not reinvent the wheel. It works storing its data in a SQL database, and it will connect to any database management system which accepts a SQLAlchemy connector. This means any reasonably modern database system and includes MySQL, PostgreSQL, Oracle. It can also work with sqlite, which, for single user purposes is quite sufficient and efficient. If you connect Ghini to a real database system, you can consider making the database part of a LAMP system (Linux-Apache-MySQL-Php) and include your live data on your institution web site.
The program was born in English and all its technical and user documentation
is first written in that language. Both technical and user documentation use
gettext, an advanced tool for semi-automatic translation.
The program has been translated and can be used in various other languages, including Spanish (97%), French (82%), Portuguese (71%), to name some Southern American languages, as well as Ukrainian (100%) and Czech (71%).
Translation of documentation goes a bit slower, with only Ukrainian, Spanish and Italian at more than 50%.
Installing Ghini on Windows is an easy and linear process, it will not take longer than 10 minutes. Ghini was born on Linux and installing it on ubuntu, fedora or debian is consequently even easier. MacOSX being based on unix, it is possible to successfully run the Linux installation procedure on any recent Apple computer, after a few preparation steps.
The installation process will produce an updatable installation, where updating it will take less than one minute. Depending on the amount of feedback we receive, we will produce updates every few days or once in a while.
Ghini is continuously and extensively unit tested, something that makes regression of functionality close to impossible. Every update is automatically quality checked, on the Travis Continuous Integration service. Integration of TravisCI with the github platform will make it difficult for us to release anything which has a single failing unit test.
Most changes and additions we make, come with some extra unit test, which defines the behaviour and will make any undesired change easily visible.
Ghini is extensible through plugins and can be customized to suit the needs of the institution.