Closed gocentral closed 9 years ago
Original comment by: jenclark
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I like ...in flowering plants.
Tanya
Original comment by: tberardini
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I suggest making it consistent with any other species/taxa. If latin goes in real term, we may have a synonym for the common name.
Original comment by: jaiswalp
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Actually I didn't mean just to standardise Magnoliophyta terms only. I was suggesting that we should reach an agreement for all sensu terms.
Thanks,
Jen
Original comment by: jenclark
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several people have written to say that they'd like English in the definition since the latin is already in the term name. If we are agreed on that then I could quickly put together a bit for the documentation that shows how each should be worded. For example 'sensu Magnoliophyta' would be 'as in flowering plants' and 'sensu mammalia' would be 'as in mammals'.
Jen
Original comment by: jenclark
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good idea- I'll retrofit the Insecta/insects definitions. Becky
Original comment by: beckyfoulger
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Rightio, thanks. I maybe better send that to the list before I go ahead and do anything.
Jen
Original comment by: jenclark
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Here is a list of the sensu groups currently being used and the pubmed entry for each:
Amphibia: Amphibia (amphibians), class, amphibians
Animalia: Metazoa (metazoans), kingdom, animals
Bacteria: Bacteria (eubacteria), superkingdom, eubacteria
Deuterostoma: no entry
Dictyosteliida: Dictyosteliida (dictyostelid cellular slime molds), order, eukaryotes
Diptera: Diptera (flies), order, flies
Drosophila: Drosophila, subgenus, flies or Drosophila (fruit flies), genus, flies
Eukarya: Eukaryota (eucaryotes), superkingdom, eukaryotes
Fungi: Fungi (fungi), kingdom, fungi
Gnetophyta: Gnetophyta, seed plants
Holometabola: Endopterygota, infraclass, insects
Insecta: Insecta (true insects), class, insects
Invertebrata: no entry but does have: Vertebrata (vertebrates), vertebrates
Magnoliophyta: Magnoliophyta (flowering plants), flowering plants
Mammalia: Mammalia (mammals), class, mammals
Nematoda: Nematoda (roundworms), phylum, nematodes
Protostomia: Protostomia, animals
Saccharomyces: Saccharomyces, genus, ascomycetes
Tracheophyta: Tracheophyta (vascular plants), vascular plants
Vertebrata: Vertebrata (vertebrates), vertebrates
Viridiplantae: Viridiplantae (green plants), kingdom, green plants
Original comment by: jenclark
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Looking up the meanings of all these sensu terms I have discovered that it's not so easy to find a succinct English version for some of them. I will keep looking. Meanwhile, here are the defs I've found so far:
Defs for each:
Amphibia: Amphibia (amphibians), class, amphibians The Amphibia are distinguished by having usually no scales, by having eggs and embryos similar to those of fishes, and by undergoing a complete metamorphosis, the young having gills. There are three living orders: (1) The tailless, as the frogs (Anura); (2) The tailed (Urodela), as the salamanders, and the siren group (Sirenoidea), which retain the gills of the young state (hence called Perennibranchiata) through the adult state, among which are the siren, proteus, etc.; (3) The Coecilians, or serpentlike Amphibia (Ophiomorpha or Gymnophiona), with minute scales and without limbs. The extinct Labyrinthodonts also belonged to this class. The term is sometimes loosely applied to both reptiles and amphibians collectively.
Animalia: Metazoa (metazoans), kingdom, animals no def
Bacteria: Bacteria (eubacteria), superkingdom, eubacteria One of the two major classes of prokaryotic organism (the other being the Cyanobacteria).
Deuterostoma: no entry
Dictyosteliida: Dictyosteliida (dictyostelid cellular slime molds), order, eukaryotes An order of protozoa characterised by their ability to aggregate to form multicellular pseudoplasmodium, which give rise to a multispored fruiting body. A stalk tube is present.
Diptera: Diptera (flies), order, flies Order of insects with one pair of wings
Drosophila: Drosophila, subgenus, flies or Drosophila (fruit flies), genus, flies A genus of small, American flies, (Genus Diptera)
Eukarya: Eukaryota (eucaryotes), superkingdom, eukaryotes The phylogenetic domain containing all eukaryotic organisms.
Fungi: Fungi (fungi), kingdom, fungi All are classified in this kingdom because they absorb food in solution directly through their cell walls and reproduce through spores. None conduct photosynthesis.
Gnetophyta: Gnetophyta, seed plants
Holometabola: Endopterygota, infraclass, insects Those insects which have a complete metamorphosis; metabola.
Insecta: Insecta (true insects), class, insects
Invertebrata: no entry but does have: Vertebrata (vertebrates), vertebrates A comprehensive division of the animal kingdom, including all except the Vertebrata.
Magnoliophyta: Magnoliophyta (flowering plants), flowering plants
Mammalia: Mammalia (mammals), class, mammals <zoology> The highest class of Vertebrata. The young are nourished for a time by milk, or an analogous fluid, secreted by the mammary glands of the mother. Mammalia are divided into three subclasses; I. Placentalia. This subclass embraces all the higher orders, including man. In these the foetus is attached to the uterus by a placenta. II. Marsupialia. In these no placenta is formed, and the young, which are born at an early state of development, are carried for a time attached to the teats, and usually protected by a marsupial pouch. The opossum, kangaroo, wombat, and koala are examples. III. Monotremata. In this group, which includes the genera Echidna and Ornithorhynchus, the female lays large eggs resembling those of a bird or lizard, and the young, which are hatched like those of birds, are nourished by a watery secretion from the imperfectly developed mammae.
Nematoda: Nematoda (roundworms), phylum, nematodes A class of unsegmented helminths with fundamental bilateral symmetry and secondary triradiate symmetry of the oral and oesophageal structures. Many species are parasites.
Protostomia: Protostomia, animals
Saccharomyces: Saccharomyces, genus, ascomycetes Genus of Ascomycetes yeasts. Normally haploid unicellular fungi that reproduce asexually by budding.
Tracheophyta: Tracheophyta (vascular plants), vascular plants A division of plants comprising green plants with a vascular system which contain tracheids or tracheary elements, being the Pteridophyta (ferns) and Spermatophyta (angiosperms and gymnosperms), commonly called vascular plants.
Vertebrata: Vertebrata (vertebrates), vertebrates One of the grand divisions of the animal kingdom, comprising all animals that have a backbone composed of bony or cartilaginous vertebrae, together with Amphioxus in which the backbone is represented by a simple undivided notochord. The Vertebrata always have a dorsal, or neural, cavity above the notochord or backbone, and a ventral, or visceral, cavity below it. The subdivisions or classes of Vertebrata are Mammalia, Aves, Reptilia, Amphibia, Pisces, Marsipobranchia, and Leptocardia.
Viridiplantae: Viridiplantae (green plants), kingdom, green plants
Original comment by: jenclark
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> Bacteria: > Bacteria (eubacteria), superkingdom, eubacteria > One of the two major classes of > prokaryotic organism (the other being > the Cyanobacteria).
hmmm, what about archaebacteria?
I'm learning a lot from this!
Original comment by: mah11
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Yes it's very informative isn't it? I'm starting to think that if it turns out to be really too complicated then it might be best just to document on the web what we mean by the sensu groups we use, and stick to using the latin in the defs. I think we might not be able to convey the whole meaning in succinct english in the def, and that leaves a choice of latin or potentially misleading english. I will keep burrowing in the literature though. Maybe there is a sensible def somewhere.
Original comment by: jenclark
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Gnetophyta: definitive def from botany book ISBN0697037754 p 721: 'the three genera that differ from all other gymnosperms in having vessels in their xylem, where gymnsperms are defined as non-flowering seed plants. Genera are Ephedra, Gnetum, Welwitschia
Original comment by: jenclark
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These seem good:
Animalia: as in the taxonomic kingdom comprising all living or extinct animals
Dictyosteliida: as in cellular slime molds
Diptera: as in the large order of insects having a single pair of wings and sucking or piercing mouths; includes true flies and mosquitoes and gnats and crane flies.
Drosophila: 'as in the fruitfly genus, Drosophila'.
Eukarya: as in organisms consisting of one or more eukaryotic cells. The most distinctive feature of the eukaryotic cell is the presence of one or more membrane-bound nuclei.
Vertebrata: as in vertebrates
Invertebrata: as in invertebrates
Original comment by: jenclark
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More good ones:
Viridiplantae: as in the kingdom of green plants, which includes green algae.
Tracheophyta: as in the vascular plants
Nematoda: as in the nematodes (could also add round worms in brackets?)
Mammalia: as in mammals.
Original comment by: jenclark
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this is fine:
Magnoliophyta: as in flowering plants
These are a bit more complicated and still need some work:
Amphibia: Quick definitions (Amphibia) frogs; toads; newts; salamanders; caecilians
Bacteria: single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission
Deuterostoma: Deuterostomia:a series of the Eucoelomata, including the echinoderms, hemichordates, and chordates, in all of which the site of the blastopore is posteriorfar from the mouth, which forms a new structure unrelated to the blastopore. Cf. Protostomia.
Fungi: Botany book ISBN047186840X says 'a thallus plant unable to make it's own food, exclusive of bacteria'
Holometabola: Endopterygota, infraclass, insects
Insecta: Insecta (true insects), class, insects
Protostomia: Protostomia, animals
Saccharomyces: Saccharomyces, genus, ascomycetes
Original comment by: jenclark
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These might do:
Protostomia: as in the series of the Eucoelomata, including the mollusks, annelids, and arthropods, in all of which the mouth arises from the blastopore. (bit complicated this one.) http://www.mercksource.com
Amphibia as in amphibians
Bacteria as in bacteria
Fungi as in fungi
Insecta as in true insects
Original comment by: jenclark
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last ones:
Holometabola as in those insects which have a complete metamorphosis
Saccharomyces as in the fungal genus Saccharomyces
Deuterostoma: as in the series of the Eucoelomata, including the echinoderms, hemichordates, and chordates, in all of which the site of the blastopore is posteriorfar from the mouth, which forms a new structure unrelated to the blastopore.
Some of these definitions seem accurate and short and would work and then a few are far too long, and I'm not sure yet what to do about those. Still thinking...
Original comment by: jenclark
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I think we can safely leave the extinct bit out of the defn of animals !
Does "bacteria" include both Arche's and Eubacteria ? May need to read/consult on that one
Drosophila should be: As in the Dipteran genus, Drosophila
Must dash - off to sit by the Med and eat fish !
Michael
Original comment by: jenclark
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Assuming we use the Woese domain classification, no, it doesn't. Archaea =/= Bacteria. The collective group would be prokaryotes.
Erich
Original comment by: jenclark
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latest shot at this:
Latest version 17/11/03
Example of plan:
Term name ends: (sensu Magnoliophyta) def ends: as in flowering plants (Magnoliophyta, taxon_id:3398)
GO.usage.html says after this bit: http://www.geneontology.org/doc/GO.usage.html\#sensu
To find the specific meaning of the grouping term used, please search on the taxon_id at the NCBI Taxon website http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/wwwtax. cgi?mode=Root&id=1&lvl=3&lin=f&keep=1&srchmode=1&unlock.
Listing of how they will all look:
Term name ends: (sensu Gnetophyta) def ends: as in the Gnetophyta (taxon_id:58022)
(Animalia) Term name ends: (sensu Metazoa) def ends: as in Metazoa (taxon_id:33208)
Term name ends: (sensu Dictyosteliida) def ends: as in Dictyosteliida (taxon_id:33083)
Term name ends: (sensu Diptera) def ends: as in Diptera (taxon_id:7147)
Term name ends: (sensu Drosophila) def ends: as in the Dipteran genus, Drosophila (taxon_id:7215)
(Eukarya) Term name ends: (sensu Eukaryota) def ends: as in Eukaryotes (Eukaryota, taxon_id:2759)
Term name ends: (sensu Vertebrata) def ends: as in vertebrates (Vertebrata, taxon_id:7742)
[Invertebrata =/ not recognised as a valid taxonomic group This one will be removed from use and should be replaced with something appropriate in each case.]
Term name ends: (sensu Viridiplantae) def ends: as in the green plants, including green algae (Viridiplantae, taxon_id:33090)
Term name ends: (sensu Tracheophyta) def ends: as in the Tracheophyta (taxon_id:8023)
Term name ends: (sensu Nematoda) def ends: as in the nematodes (Nematoda, taxon_id:6231)
Term name ends: (sensu Mammalia) def ends: as in mammals (Mammalia, taxon_id:40674)
Term name ends: (sensu Magnoliophyta) def ends: as in flowering plants (Magnoliophyta, taxon_id:3398)
Term name ends: (sensu Amphibia) def ends: as in amphibians (Amphibia, taxon_id:8292)
Term name ends: (sensu Eubacteria) def ends: as in the Eubacteria (Bacteria, taxon_id:2)
Fungi Term name ends: (sensu Fungi) def ends: as in the Fungi (taxon_id:4751)
Term name ends: (sensu Insecta) def ends: as in the true insects (Insecta, taxon_id:50557)
(Holometabola) Term name ends: (sensu Endopterygota) def ends: as in those insects which have a complete metamorphosis (Endopterygota, taxon_id:33392)
Term name ends: (sensu Saccharomyces) def ends: as in Saccharomyces (taxon_id:4930)
(Deuterostoma) Term name ends: (sensu Deuterostomia) def ends: as in Deuterostomia (taxon_id:33511)
Term name ends: (sensu Protostomia) def ends: as in Protostomia (taxon_id:33317)
Original comment by: jenclark
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the latest plan:
<p> Listing of how they will all look: </p>
<p> Term name ends: (sensu Gnetophyta) <br>def ends: as in the taxon Gnetophyta (Gnetophyta, Taxonomy_ID:58022) </p>
<p> (Animalia) Term name ends: (sensu Metazoa) <br>def ends: as in the taxon Metazoa (Metazoa, Taxonomy_ID:33208) </p>
<p> Term name ends: (sensu Dictyosteliida) <br>def ends: as in the taxon Dictyosteliida (Dictyosteliida, Taxonomy_ID:33083) </p>
<p> Term name ends: (sensu Diptera) <br>def ends: as in the taxon Diptera (Diptera, Taxonomy_ID:7147) </p>
<p> Term name ends: (sensu Drosophila) <br>def ends: as in the taxon Drosophila (Drosophila, Taxonomy_ID:7215) </p>
<p> (Eukarya) Term name ends: (sensu Eukaryota) <br>def ends: as in the taxon Eukaryota (Eukaryota, Taxonomy_ID:2759) </p>
<p> Term name ends: (sensu Vertebrata) <br>def ends: as in the taxon Vertebrata (Vertebrata, Taxonomy_ID:7742) </p>
<p> [Invertebrata =/ not recognised as a valid taxonomic group<br> This one will be removed from use and should be replaced with something appropriate in each case.] </p>
<p> Term name ends: (sensu Viridiplantae) <br>def ends: as in the taxon Viridiplantae (Viridiplantae, Taxonomy_ID:33090) </p>
<p> Term name ends: (sensu Tracheophyta) <br>def ends: as in the taxon Tracheophyta (Tracheophyta, Taxonomy_ID:8023) </p>
<p> Term name ends: (sensu Nematoda) <br>def ends: as in the taxon Nematoda (Nematoda, Taxonomy_ID:6231) </p>
<p> Term name ends: (sensu Mammalia) <br>def ends: as in the taxon Mammalia (Mammalia, Taxonomy_ID:40674) </p>
<p> Term name ends: (sensu Magnoliophyta) <br>def ends: as in the taxon Magnoliophyta (Magnoliophyta, Taxonomy_ID:3398) </p>
<p> Term name ends: (sensu Amphibia) <br>def ends: as in the taxon Amphibia (Amphibia, Taxonomy_ID:8292) </p>
<p> Term name ends: (sensu Eubacteria) <br>def ends: as in the taxon Eubacteria (Bacteria, Taxonomy_ID:2) </p>
<p> Fungi Term name ends: (sensu Fungi) <br>def ends: as in the taxon Fungi (Fungi, Taxonomy_ID:4751) </p>
<p> Term name ends: (sensu Insecta) <br>def ends: as in the taxon Insecta (Insecta, Taxonomy_ID:50557) </p>
<p> (Holometabola) Term name ends: (sensu Endopterygota) <br>def ends: as in the taxon Endopterygota (Endopterygota, Taxonomy_ID:33392) </p>
<p> Term name ends: (sensu Saccharomyces) <br>def ends: as in the taxon Saccharomyces (Saccharomyces, Taxonomy_ID:4930) </p>
<p> (Deuterostoma) Term name ends: (sensu Deuterostomia) <br>def ends: as in the taxon Deuterostomia (Deuterostomia, Taxonomy_ID:33511) </p>
<p> Term name ends: (sensu Protostomia) <br>def ends: as in the taxon Protostomia (Protostomia, Taxonomy_ID:33317)
</p>
<h3>Documentation</h3> <p> GO.usage.html addition to this section: http://www.geneontology.org/doc/GO.usage.html\#sensu </p>
<p> To find the specific meaning of the taxonomic group term used, please search on the Taxonomy_ID at the <a href="http:// www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/wwwtax. cgi?mode=Root&amp;id=1&amp;lvl=3&amp;lin=f&amp;keep=1& amp;srchmode=1&amp;unlock"> NCBI Taxonomy website</a> or for specific terms that are currently in use refer to the NCBI Taxonomy pages shown below. </p>
<a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=58022&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Gnetophyta, Taxonomy_ID:58022</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33208&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Metazoa, Taxonomy_ID:33208</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33083&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Dictyosteliida, Taxonomy_ID:33083</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=7147&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Diptera, Taxonomy_ID:7147</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=7215&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Drosophila, Taxonomy_ID:7215</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=2759&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Eukaryota, Taxonomy_ID:2759</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=7742&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Vertebrata, Taxonomy_ID:7742</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33090&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Viridiplantae, Taxonomy_ID:33090</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=8023&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Tracheophyta, Taxonomy_ID:8023</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=6231&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Nematoda, Taxonomy_ID:6231</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=40674&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Mammalia, Taxonomy_ID:40674</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=3398&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Magnoliophyta, Taxonomy_ID:3398</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=8292&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Amphibia, Taxonomy_ID:8292</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=2&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Bacteria, Taxonomy_ID:2</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=4751&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Fungi, Taxonomy_ID:4751</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=50557&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Insecta, Taxonomy_ID:50557</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33392&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Endopterygota, Taxonomy_ID:33392</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=4930&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Saccharomyces, Taxonomy_ID:4930</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33511&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Deuterostomia, Taxonomy_ID:33511</a><br> <a href="http://www.ncbi.nlm.nih.gov:80/Taxonomy/Browser/ wwwtax.cgi?mode=Info&id=33317&lvl=3&lin=f&keep=1&srchmode=1& unlock"> Protostomia, Taxonomy_ID:33317</a><br>
Original comment by: jenclark
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The documentation on this has now been agreed and added to the website so we are free to begin the retrofit.
Jen
Original comment by: jenclark
Original comment by: jenclark
Does anybody have any preference about the wording of sensu definitions? Some currently end:
... as in flowering plants
or
... as in Magnoliophyta
I'd be keen to know which is favoured between latin and English so I can keep my definitions consistent.
Jen
Reported by: jenclark
Original Ticket: "geneontology/ontology-requests/1292":https://sourceforge.net/p/geneontology/ontology-requests/1292