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ghini

I have put this page together as I have found ghini (and bauble its predecessor) very useful in cataloguing my own small collection of plants.
I hope that it may encourage others to use, or at least try it, too.

ghini and its predecessor bauble have been hidden away for too long!.

This is taken from the beginning of the documentation page...
Ghini is an application for managing botanical specimen collections. With it you can create a searchable database of plant records.

bauble was started many years ago as an application to catalogue plants at Belize Botanical Gardens so perhaps seems a bit over the top for gardeners and collectors at home but that is definitely not the case.

The application can record an immense amount of data on any plant. Many of the included fields will be useful to gardeners and collectors, along with the ability to add notes providing, for example, a history of the life of each plant.

Installation and general usage is set out in the above linked documentation but I will run through my installation and usage so far, step by step.

(Note that all images are links for viewing at full size if required.)

Installation

I have performed three or four installs here on debian and raspbian (Raspberry Pi) systems and generally they have been successful as described in the documentation, however my last on a Pi was not so smooth but cured by installing python-all and python-all-dev - a bit overkill perhaps!

As well as linux, installation instructions are given for Windows and Mac. I have no experience of these but the instructions look to be comprehensive.

The application builds during the install process and is automatically installed into a virtual environment in the user's home directory. The resulting application is run from a script in the /bin directory, again within the user's home directory.

First run

On first running ghini (./bin/ghini in linux and run ./bin/ghini -u to update to the latest version) we are presented with a dialogue window similar to the one on the right although this image is of my own populated database named Plants.
Creating a new database called test after clicking the Add button. (The procedure is similar when creating our initial test database.)
The result of clicking OK in the previous dialogue which shows our new database name and gives us a choice of database back-end to choose from (choice may depend on what you have installed on your own system). For this exercise we will leave the default choice of SQLite. SQLite is fairly easy to manage, very easy to backup or copy to another machine/location eg. for use on a portable device. We will also leave Use default locations as suggested.
Clicking Connect produces a warning that we have an empty database, clicking OK here brings up a new dialogue.
Clicking Yes here will create and populate our new database with the program's defaults including many Families and Genera^[1]. It may take some seconds for this operation to complete. We will also be asked to fill in Institution details but this only requires the basics in order to continue eg. Home. If we enter an email address and click Register we will receive a single welcome mail from the developers. Our new database (and other files) will be placed in your .bauble or .ghini directories.

We are now at the point where we can enter our first data.

^[1]
Included is 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 used by permission of RBG Kew.

Entering data

Adding Species

I have picked out one of my plants to use as an example entry. It was labelled Scilla violacea when purchased from a local garden centre on 22 Feb 2016 and I re-potted it on 26 Feb 2016.

Note: It is very tempting to add a new plant starting by adding either a Family or Genus but as these fields are very well populated already this would be a mistake.

We start from Insert -> Species. Enter violacea in the Species field and start to type Scilla in the Genus field. As we type each letter a list of possible matches will be shown, the more we type the fewer the available choices, we select Scilla. Clicking the green button checks the entry against The Plant List database and gives us the option of adding additional data as shown here. The first suggestion adds author information to this entry, the second will add Ledebouria socialis, the officially correct name for Scilla violacea, as another species in our database. We are going to accept both of these suggestions. Infraspecific parts allows entry of subsp., var. etc., self-explanatory I'm sure but see here for more information. Note: I came across an issue adding Gymnocalycium damsii in that the query responds No match found on ThePlantList.org. The Plant List does in fact have an entry for Gymnocalycium damsii but it is listed as synonym of Gymnocalycium anisitsii subsp. damsii. The version I am using at present does not support this type of query - or produce a very informative response. A future version will likely address this but may still inform you that it cannot handle this type of query. The solution is to add Gymnocalycium anisitsii supsp. damsii and set Gymnocalycium damsii as a synonym, a little manual intervention but produces the correct result.
This shows a cropped dialogue image with the author data added. At this point we could click OK to complete the entry, or click Add Accessions to add a specimen actually in our collection or Next to add another Species but let's take a look at the other tabs first.
This is the Additional info tab and as you can see I have added a few entries. Label distribution is a field for data to be printed on labels and need not be as geographically specific as Distribution. Habit I have found of little use for my own plants (I haven't found a source of definitive botanical information relating to cacti and succulents as yet). Vernacular Names allows entry of common names in various languages. Synonyms is of more interest to us (note that this field will only accept an entry of another species in our database). We will take a look at this field in a moment but now we click OK to enter this Species and the data we have added into our database.
Earlier we accepted the option to add Ledebouria socialis to the database, so we should now have two Species entries in total, Scilla violacea and Ledebouria socialis. Checking the Home screen we now see 2 in the Species line, clicking on the 2 should show the Species screen with entries for both Scilla violacea and Ledebouria socialis.
We can see here that Scilla violacea has been added as a synonym of Ledebouria socialis (this is a clickable link).
Let's take a look at the Edit dialogue for Ledebouria socialis. Note the author field has already been auto-filled by ghini as the Species was added.
Scilla violacea has been entered as a synonym within the Synonyms field. We can add Distribution and Vernacular Names data to this entry if we so desire.

Notes and Pictures tabs are probably self-explanatory but we will look more closely at Notes in the Insert -> Plant section.

Click OK to add the species to our database and close the dialogue window.

Adding Accessions

Accession is a term I had not come across previously in terms of plants and collections but it is very important in botanical cataloguing. The simplest definition would seem to be that a unique specimen group is called an Accession.

I have been using Accession for my acquisition of a plant. Each plant in my collection has come from somewhere, a nursery, garden centre, shop, another collector etc. As such it is unique from any specimen of the same species obtained elsewhere or at another time.

If I obtain another plant of the same species as one I have already then I treat it as another Accession unless multiples are obtained at the same time and from the same place.

A better description of Accession and some some of the other terms and how it all fits together is given in this PDF document from the National Botanic Gardens, Glasnevin, Dublin, Ireland.

Our Home screen now looks like this. Note the non-grey numerics in the various columns. These numerics are links to other screens.
Clicking on the number 2 in the Species line with first entry highlighted.
The second entry highlighted.
An Accession can be added using any of the following methods Insert -> Accession Add Accession from the highlighted entry in the Species screen from the Species editor dialogue. In our particular case, as we have a synonymous name, choosing which species entry to add the Accession to depends on how we wish to label or catalogue your plants. We will stick with Scilla violacea in this example. (It is very easy to switch from an entry to its synonym from links within the Species screen.) The first part of Accession ID can be usefully changed to suit the year we acquired this specimen. The second part will increment as we add a new Accession. Date Accessioned and Date Received I set to the date a specimen entered my collection, invariably they are the same. (If I don't have an exact date for some older specimens I use a date such as 01-01-2015.) Note: Accession ID can be changed in later edits if desired and this change will be reflected in all Plants under this Accession. The new Accession ID must be unique!
The Source tab allows us to add details of where we obtained our specimen. We haven't entered any Sources so far so click on New and enter details as required.
On clicking OK the new entry will appear in the main Contact field and be available in a drop-down list in future Source entries. The Verifications and Vouchers tabs are not really of use to us as gardeners or collectors.

Adding Plants

A Plant can be added using one of the following methods

Insert -> Plant
Add Plant from the highlighted entry in the Accessions screen
from the Accessions editor dialogue

Adding a Plant requires a defined Location ie. where it is physically placed, if no Locations have been defined as we add our first Plant then a prompt will open a dialogue.
Enter a suitable location name, perhaps Greenhouse and code GH (this dialogue provides yet another way to add a Plant.).

New location dialogue.
This is the main Plant editor screen. Accession is the ID created at the point of adding the Accession Plant code usually starts at 1 in each Accession and auto-increments. Quantity is usually 1 however sometimes there may be more than one plant in a pot, leaves or stems may break off that can be treated as vegetative parts or we may acquire more than one of a species from the same Source at the same time. A number greater than 1 will add more than 1 Plant entries (this does not seem to be consistent at present - or perhaps it was just my imagination that it happened once). You may notice in this image that for Location I have used Living Room not Greenhouse as entered earlier. I always try and quarantine new plants before mixing them with the rest and often they are quarantined on my living room window cill.
The Propagation tab can be used to record specific details when propagating a plant.
This is how the Propagation tab looks after filling in the above details.
The newly propagated plant is a new Accession and requires creating.
The Source of this new new Accession is Garden Propagation and Plant ID refers back to the parent plant whose propagation details we filled in earlier.
The Notes editor screen where we can add any number of notes. It is probably of little worth entering anything in the User field if we are the only person likely to be using our database. A Category must be entered, this can be anything you like. This new Category will be added to a drop-down list in future Notes. The text of our Note is added below. If a URL is entered in a Note it will be available as a clickable link in the appropriate main screen (I use Category name Web for these). Note: The Notes dialogue is similar for Family, Genus, Species and Accession but the Note and drop-down list of Categories will be unique to each. The Pictures tab allows addition of images, see the documentation. Pictures can also be added to Species entries. They will be displayed in the centre section of the Species and other screens - this may require dragging the section border across to expose.

Results so far

We have now run through the basic features so let's take a look at the results.

The Home screen shows our entries. Any field with a non-grey numeric value the total, in use or unused columns can be clicked on to take us to the relevant list of included items. A search term can be entered in the search field at the top of the window. Try scilla for example or 2016.
stored queries are a little more complicated, see the documentation. Here is a stored query that I use frequently, it is based on a result from the Query Builder (see the Home screen) but note that notes.date does not actually appear within the Query Builder dialogue and has to be added manually. The query searches for all Plants that have a Note containing the Category Repotted and a date later than 2016-06-01. It displays a list of all matching Plants. (The date can be edited from command line as well as the stored queries edit dialogue.)
This is the Species screen as linked from the Home screen. We see the two species we have entered, the Scilla entry has been expanded using the arrow head markers to the left. This shows any Accessions and Plants, these items can be edited. Note that there is a currently hidden pane in the centre that can be expanded by dragging to show any Pictures added to our various entries.
This is an image of the label format I currently use for 12mm wide tapes. The barcode is generated from the Plant ID (I use QRencode for its compactness) and Plant ID is repeated in human-readable form beneath the textual binomial. With the cursor placed in the search field of the Home screen, scanning a barcoded label will immediately show me the relevant Plant. Note: I create a csv file suitable for label printing from a slightly modified plant_list Report, adding quotes and a comma field delimiter for each field. The text can be extracted from the generated pdf Report file and massaged if need in a text editor.

Reports

The included Reports are rather basic but good enough to produce plant lists and simple labels.
The .xsl templates can be edited and other fields added but this may mean searching through the install files to find a list of useful/usable field-names.
There is also the possibility of using the Mako Report Formatter but I haven't played with that at all so far.

Additional notes

If we set a Plant's Quantity as 0 as perhaps we no longer have it in our collection (we could also mark as Dead or Given Away etc.) its highlighted colour will change in the Plant screen.

It is possible to change the Species of a Plant very easily.
For example: perhaps we have sown some seed and one emerges as a stinging nettle (Urtica dioica)!
We would first have to Add Accession for Urtica dioica then, remembering its Accession ID, use that in place of the Accession ID shown in the Plant edit dialogue, its Plant code will remain the same but can also be changed as long as it is unique.