Taxonomy and Hierarchical Keywords

This morning I checked my email and also did some more reading about Taxonomy and Hierarchical Keywords. Reading this thread Catalog Sets and hierarchical / non-hierarchical keywords, it seems that Microsoft Expression Media (formerly iView Media Pro) can do this, but unfortunately there wasn't any discussion in that thread about doing this in Adobe Bridge.



After some more googling I found that in Lightroom you can actually add synonyms for Hierarchical (or normal) keywords: Keywording Photographs, Part 2 Importing Keyword Files and Lightroom and Keywords Part V - Synonyms. Unfortunately it seems these synonyms are only stored in Lightroom's local database, and only added to an image as a normal keyword upon 'export'. If you will only ever use Lightroom to edit/view metadata on your images, then this is probably okay, but for me I need a way to extracting the Hierarchical keywords on the web server, plus I don't use Lightroom and don't like to be stuck using one program.

I think that probably what I will do is to arrange my Hierarchical keywords in the format Latin name (Common name; Alternate name 1), then in my custom XMP File Info panel, provide a way for extracting the individual keywords from the Hierarchical Keywords into the (normal) keywords field. This way the Hierarchical keywords maintain the link between the Latin name, common name and any alternate names.

Using the Begonia example again, the Hierarchical keywords would look like:


With the way I was previously intending to use Hierarchical Keywords to represent the taxonomy of the subject of an image, there was no way within the Hierarchical Keywords of showing that, say 'Plants' was a synonym of 'Plantae'. If you only have one taxonomic hierarchical category/keyword assigned to an image, it can be inferred that the top level Common name must be a synonym of the top level Latin name, and so on for lower category levels.

However, you would have a problem if your image featured multiple subjects that you wanted to add Taxonomic hierarchical keywords for, e.g. a photo of a duck and a pigeon


My plan was to use photoshop:SupplementalCategories to hold info on the lowest hierarchical level's Latin and Common names. When you know that the lowest levels of both the Common name and Latin name hierarchies are synonymous, then you can infer that hierarchical keywords in the upper levels for the Common name and Latin name hierarchies are also synonymous, e.g.


I don't think this method is that great though, which is why I think I'll probably go with Taxonomic Hierarchical keywords in the form I described earlier in this post.



After that I noticed that when I looked at the metadata for an image using my custom XMP File Info Panel in Bridge, the Lens used for taking the image was being added to the end of the list of possible lenses, rather than the existing entry for that lens being selected.

Looking at my code for the Lens combo box, I thought I had found the reason - in the list of lenses, the lens name starts with the Manufacturer, but the lens name recorded in the aux:Lens field of the XMP by ACR, didn't include the manufacturer.

So I changed my code to check whether the aux:Lens value existed anywhere in the list of lenses, rather than matching the whole field. I had quite a bit of trouble getting this to work, as I was using indexOf(), which I thought would return false if the Lens name didn't exist, but after a lot of messing about, turns out it returns -1 if the string can't be matched.

However, after working that out, I found the lens was still being added to the list. The problem was that the aux:Lens had the lens name as "EF100mm f/2.8 Macro USM", whilst I had the lens name as "Canon EF 100mm f/2.8 USM Macro". So the value Adobe Camera Raw had added to the image doesn't have a space between EF100mm, whilst the value in my list doesn't, hence they weren't matching.

So far as I'm aware, there should be a space between "EF" and "100mm", so rather than change my list values to match the ones given by ACR, I decided to just undo all my changes and put it back as it was before. It won't be hard to select all images and choose the lens used manually, rather than having my panel choose the value automatically from the value saved by ACR (which is what I was trying to do).

After lunch I went on Animal Crossing, and then wrote most of this blog post. When I was looking for the taxonomic hierarchy for a Wood Pigeon, I found that the hierarchy and Taxonomic names given by Fauna Europaea and Integrated Taxonomic Information System (ITIS) are quite different. There is also a slight difference between the ITIS and Encyclopedia of Life (EOL) Taxonomic hierarchies. For example, for Wood Pigeon:

• Fauna Europaea (Taxonomic Hierarchy version 1.3) lists:
  Animalia
  Eumetazoa
  Chordata
  Vertebrata
  Gnathostomata
  Aves
  Passerae
  Columbimorphae
  Columbiformes
  Columbi
  Columboidea
  Columbidae
  Columba
  palumbus
• Encycolpedia of Life lists:
  Animalia
  Chordata
  Aves
  Columbiformes
  Columbidae
  Columba
  Columba palumbus
  
  At the top right of the page it also says

  Showing authoritative information

• Catalogue of Life lists:
  Animalia
  Chordata
  Aves
  Columbiformes
  Columbidae
  Columba
• ITIS lists:
  Animalia
  Chordata
  Vertebrata
  Aves
  Columbiformes
  Columbidae
  Columbinae
  Columba Linnaeus
  Columba palumbus
• Searching the International Commission on Zoological Nomenclature (ICZN) for "Columba palumbus", I just got three results about fleas.

The most notable difference between Fauna Europaea and the other sites is the subclass "Passerae". Looking it up on Wikipedia, it says

The "Passerae" were a proposed "parvclass" of birds in the Sibley-Ahlquist taxonomy. This taxon is a variation on the theme of "near passerines", birds that were - and often still are - believed to be close relatives of the passerines (perching birds, which include the songbirds). This proposed taxon was roundly rejected by subsequent cladistic analyses.

Yet according to Fauna Europaea, the taxonomic status of Passerae is valid.

Googling for "Passerae", I didn't come across any websites saying that it isn't a valid Taxon name, but I did find this website that does list it, plus a load of other Taxonomic ranks that none of the other websites I looked at featured: Ontology Online.

I was going to say that I'm inclined to use Fauna Europaea for Taxon ranks and names, ITIS and wikipedia for Common names / Synonyms of Latin/Scientific names, but I just noticed the last update on Fauna Europaea is 19 April 2007, whilst ITIS was last updated 08 January 2009, which, while not particularly recent, is still a lot more recent than April 2007.

Having said that, the data that ITIS uses seems to be mostly from before 2001. Fauna Europaea does also seem to make itself out to be an authoritative resource:

The Fauna Europaea project has assembled a database of all European land and freshwater animals. Experts in taxonomy have provided data of all species currently known on the European continent and associated areas. The main building-blocks of the Fauna Europaea database are the family taxa that have been established beforehand. The contributing experts delivered data on all taxa below the family level.

A default taxonomic higher hierarchy was thus needed to provide a framework for the lower taxa. This standard hierarchy has been established with the help of leading European taxonomists and reviewed by the Fauna Europaea Taxonomic Advisory Team.

Although limited by its original, practical scope (providing a management tool), its scientific scope (representing the temporal view of a restricted number of European experts), and its geographic scope (taxa not present within Europe are excluded, as are marine taxa), the taxonomic hierarchy thus established may serve as an authoritative standard for taxonomy in Europe.

I looked at WikiSpecies and Encyclopedia of Life. WikiSpecies seems to have many Taxanomic ranks, whilst EOL seems to only have a few Taxanomic ranks. WikiSpecies doesn't seem to have any particular people working on it (at least I didn't see it mentioned anywhere), while EOL says

The EOL staff is made up of scientists and non-scientists working from museums and research institutions around the world.

I think that maybe I will use EOL in organising my images by taxon.

As well as looking at that in the evening, I also changed my custom XMP File Info Panel so it had a button to get keywords from the Hierarchical Keywords already assigned to it.

The weather was a mixture of clouds and a bit of sun. It looked like there was a decent sunset.

Food
Breakfast: Blackcurrant jam toast sandwich; cup o' tea.
Lunch: Mature cheddar cheese with sweet & crunchy salad sandwich made with fresh bread-maker-made bread; honey on slice of fresh bread-maker-made bread; cherry; banana; Rocky; cup o' tea.
Dinner: Jacket potato; baked beans & sausages; grated mature cheddar cheese. Pudding was weird cherry stuff that Moccle and Lad made - kind of like bread & butter pudding except if the bread was all mushed up into the milky eggy stuff instead of being allowed to go a bit toasty/crispy in places, and with cherries. Coffee; 3 pieces of Sainsbury's caramel chocolate.
Supper: Coffee; choc chip cookie; nice.