Tags, Metrics and Advanced Search
The Advanced Search page allows searching by taxonomic group, geological age and citation details and can return lists of species with or without images and citations.
To allow searching by morphological criteria we have now added a large database of morphometric data and morphological tags. The coverage for this is nearly complete for the Extant and Cenozoic, but the Mesozoic has not yet been done - and the whole system is still under development (Sept 2017). Feedback is very welcome (you can use the forum page).
Tags for a species (Futyania petalosa) on a species page.
Using advanced search - some advice
- It is a bit complex so it is worth experimenting slowly.
- If you add lots of parameters you may not get any results.
- You need to choose which "module" to search (Cenozoic, Mesozoic or the Catalog), and not all searches are possible on all modules.
- If you attempt a search which is not possible you will get an error message - this should tell you what the problem was.
- Do try changing the output mode!
- Use the help text from the big blue question marks.
- A search summary appears below the search button, this should help you understand the search and see if it is what you intended
Tag and metrics options as they appear on the advanced search page, along with the search summary
Within the database the full hierarchy of parent taxa is stored for each taxon - e.g. "Syracosphaerales/Rhabdosphaeraceae/Cyrtosphaera/Cyrtosphaera aculeata". The Within taxa search option allows you to search this and so find e.g all taxa belonging to the Rhabdosphaeraceae.
Likewise the full formal taxonomic citation [e.g. Cyrtosphaera aculeata (Kamptner 1941) Kleijne, 1992] is stored in one database field and can be searched using the Citation includes option. You can use this to e.g. find taxa described by a particular author.
The primary data here are
- Lith size: estimates of maximum and minimum coccolith or nannolith size. This usually body coccolith length, or maximum dimension of nannolith. The main exceptions to this are Rhabdosphaeraceae (spine height) and Scyphosphaera (equatorial coccolith height), other exceptions are indicated in the sources text field.
- Segments per lith: Estimates of maximum and minimum number of segments per coccolith or nannolith. For holococcoliths data is number of blocks seen in cross-polars. This data is included for all nannoliths but is lacking for most heterococcoliths with >20 segments. NB Typically nannofossils consist of several cycles of elements with the same number of elements in each cycle. Hence a segment is one set of elements. Elements per cycle wold be another term for this. For nannoliths formed of a single crystal unit but with radial symmetry the number is the symmetry repeat - e.g. Tribrachiatus is recorded as having 3 segments.
- Coccosphere size: Estimates of maximum and minimum diameter of the coccosphere. This includes the coccoliths (i.e. it is not cell size) but excludes apical spines. Exceptions are noted in the sources (e.g for a few species only cell-size data was available).
- Liths per sphere: Estimates of maximum and minimum number of coccoliths per coccosphere.
- Sources: A summary of where the data came from. The prime sources are specimens illustrated on Nannotax ("illustrated specimens") and the original description ("OD"), as available from the Farinacci & Howe catalog. For Isochrysidaceae and Coccolithaceae this field is usually blank but these were the sources used. Where other sources are used these are listed.
It should be noted that the metrics are at this stage a rather rapidly produced compilation and need review and update. The objective would be for the range estimates to encompass the vast majority of species but exclude rare exceptionally small or large specimens (top/bottom 5%). In practice the estimates are probably skewed toward larger specimeens as these are most often illustrated, especially in LM. In some case range-estimates have been extended to give likely range without any direct evidence (e.g if an original author quoted a size range of 9-10µm this may have been extended to 8-11µm, this is noted in the source notes as "range extended").
On the Advanced Search page sliders are used to constrain the search to taxa of particular size ranges.
Tags are descriptive terms for an aspect of the morphology. They are designed to allow searches such as for "elliptical coccoliths with a cross in the central-area ". To build up the tags and to help users find them they are classified into tagsets covering different aspects of coccolith morphology. Each taxon may have several tags in a tagset, or indeed none. So this is not a classic character matrix, but there is so much variation been taxa that it was not possible to produce a single simple matrix and this scheme was the simplest one we could devise.
On the Advanced Search page dropdown menus are used to constrain the search to taxa which have been tagged with particular tags.
Tags for the main part of the lith
Tags for the central-area and process
- basic_shape: the main heterococcolith shapes (placolith, murolith, planolith) vs holococcoliths vs nannoliths (radiate vs others). Virtually every species has just one tag from this set.
- shape_modifier: a qualifier to the basic shape term (H: indicates holococcolith specific terms, N: nannolith specific)
- plan_view_shape: Shape of outline of lith in plan view.
- rim_or_ray_details Aspects of the rim of coccolths or rays of nannoliths (H: holococcolith specific terms, N: nannolith specific).
Tags for the coccosphere
- central-area: central-area structures and details, except spines. (H: holococcolith specific terms)
- process: Terms describing the central spine, boss, or process.
Tags for crystallography/appearance in cross-polarised light
- coccosphere_shape: Shape of the coccosphere.
- lith_types: types of cocoliths present on the coccosphere, using the standrd abbreviaitons BCc (body coccolith), CFC (circum-flagellar coccolith) etc. NB All cocccospheres have body coccoliths so these are not listed.
- V-units: Parts of the coccolith which are formed of V-units, and so are dark in plan view in xpl
- R-units: Parts of the coccolith which are formed of R-units, and so are bright in plan view in xpl, and show length-fast behaviour in their top-left corner.
- T-units: Parts of the coccolith which are formed of T-units, and so are bright in plan view in xpl, and show length-slow behaviour in top-left corner.
- optic_details: Details of appearance in cross-polarised light (xpl)
Further explanation. Notes have been given described explaining each tag and tagsets. These are included on the Advanced Search page as tooltips - i.e. if you hover over the text then after a slight delay a little box will appear explaining the term - like this. For more explanation of the terms see the Young et al. 2003 Terminology Guide, on the INA website and via the Links Menu. In principle a tag should be present for all species it could apply to and if not this is indicated (E.g. "disk-like" is applied only to holococcoliths).
example of a tooltip - short explanations like this are available for every term.
Tags as a summary of morphology
Taken together the tags provide a sort of summary of the morphology. However, this is essentially accidental and does not always work, for various reasons. First, morphological characters only shown by one or two species are generally excluded, even though they may be important and distinctive. This proved necessary in order to keep the total number of tags reasonable. Second, qualitative characters based on e.g. the relative size of structures have mostly been avoided since they are ambiguous, even though they are often important parts of species definitions. Third, the tags often overlap, e.g. a taxon may have tags for both cross and axial-cross, because either term might be searched for. Or it may have plan_view_tags such both elliptical and circular outline (since specimens may show both). Indeed tags can even seem contradictory - for instance many taxa are tagged as have the central-area both vacant and with a grill - this is because they have delicate grills which are are often missing so a user might reasonably search either for grill or vacant depending on the preservation and means of observation. So, remember tags are designed primarily for searching and the tagset may seem like an odd description of the taxon.
Likewise the tags are not designed as an identification key. In some cases it is possible to identify a species purely from its tags but more often a search will recover a range of possibilities and tags are meant to include all species which might fit. For example all Lophodolithus species have almost the same tags
Development and feedback
The tags, and metrics, have been compiled for this website and are not well-tested. This has been a major effort; there are 15,000 tags in the database and 4160 metrics and here are almost certainly numerous mistakes, omissions and imperfections in the data. If you find it useful please do review the data on taxa you know and send us suggestions for corrections. Any feedback on use of the system would also be appreciated. This can be done as comments on individual taxon pages, as comments on the forum page or by email to email@example.com.
Likewise the next project needs to be to develop tags and metrics for the Mesozoic taxa and assistance in doing this would be useful.