standardizing sensu definitions

gocentral commented 20 years ago

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

gocentral commented 20 years ago

assigned_to: nobody --> jenclark

Original comment by: jenclark

gocentral commented 20 years ago

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I like ...in flowering plants.

Tanya

Original comment by: tberardini

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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good idea- I'll retrofit the Insecta/insects definitions. Becky

Original comment by: beckyfoulger

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

<zoology> One of the classes of Arthropoda, including those that have one pair of antennae, three pairs of mouth organs, and breathe air by means of tracheae, opening by spiracles along the sides of the body. In this sense it includes the Hexapoda, or six-legged insects and the Myriapoda, with numerous legs. See Insect.
<zoology> In a more restricted sense, the Hexapoda alone. See Hexapoda.
<zoology> In the most general sense, the Hexapoda, Myriapoda, and Arachnoidea, combined. The typical Insecta, or hexapod insects, are divided into several orders, viz., Hymenoptera, as the bees and ants; Diptera, as the common flies and gnats; Aphaniptera, or fleas; Lepidoptera, or moths and butterflies; Neuroptera, as the ant-lions and hellgamite; Coleoptera, or beetles; Hemiptera, as bugs, lice, aphids; Orthoptera, as grasshoppers and cockroaches; Pseudoneuroptera, as the dragon flies and termites; Euplexoptera, or earwings; Thysanura, as the springtails, podura, and lepisma. See these words in the Vocabulary.

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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

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the latest plan:

Listing of how they will all look:

Term name ends: (sensu Gnetophyta) def ends: as in the taxon Gnetophyta (Gnetophyta, Taxonomy_ID:58022)

(Animalia) Term name ends: (sensu Metazoa) def ends: as in the taxon Metazoa (Metazoa, Taxonomy_ID:33208)

Term name ends: (sensu Dictyosteliida) def ends: as in the taxon Dictyosteliida (Dictyosteliida, Taxonomy_ID:33083)

Term name ends: (sensu Diptera) def ends: as in the taxon Diptera (Diptera, Taxonomy_ID:7147)

Term name ends: (sensu Drosophila) def ends: as in the taxon Drosophila (Drosophila, Taxonomy_ID:7215)

(Eukarya) Term name ends: (sensu Eukaryota) def ends: as in the taxon Eukaryota (Eukaryota, Taxonomy_ID:2759)

Term name ends: (sensu Vertebrata) def ends: as in the taxon Vertebrata (Vertebrata, Taxonomy_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 taxon Viridiplantae (Viridiplantae, Taxonomy_ID:33090)

Term name ends: (sensu Tracheophyta) def ends: as in the taxon Tracheophyta (Tracheophyta, Taxonomy_ID:8023)

Term name ends: (sensu Nematoda) def ends: as in the taxon Nematoda (Nematoda, Taxonomy_ID:6231)

Term name ends: (sensu Mammalia) def ends: as in the taxon Mammalia (Mammalia, Taxonomy_ID:40674)

Term name ends: (sensu Magnoliophyta) def ends: as in the taxon Magnoliophyta (Magnoliophyta, Taxonomy_ID:3398)

Term name ends: (sensu Amphibia) def ends: as in the taxon Amphibia (Amphibia, Taxonomy_ID:8292)

Term name ends: (sensu Eubacteria) def ends: as in the taxon Eubacteria (Bacteria, Taxonomy_ID:2)

Fungi Term name ends: (sensu Fungi) def ends: as in the taxon Fungi (Fungi, Taxonomy_ID:4751)

Term name ends: (sensu Insecta) def ends: as in the taxon Insecta (Insecta, Taxonomy_ID:50557)

(Holometabola) Term name ends: (sensu Endopterygota) def ends: as in the taxon Endopterygota (Endopterygota, Taxonomy_ID:33392)

Term name ends: (sensu Saccharomyces) def ends: as in the taxon Saccharomyces (Saccharomyces, Taxonomy_ID:4930)

(Deuterostoma) Term name ends: (sensu Deuterostomia) def ends: as in the taxon Deuterostomia (Deuterostomia, Taxonomy_ID:33511)

Term name ends: (sensu Protostomia) def ends: as in the taxon Protostomia (Protostomia, Taxonomy_ID:33317)

<h3>Documentation</h3> GO.usage.html addition to this section: http://www.geneontology.org/doc/GO.usage.html\#sensu

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.

<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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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>

Original comment by: jenclark

gocentral commented 20 years ago

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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

gocentral commented 20 years ago

status: open --> clockerlabs/

Original comment by: jenclark

geneontology / go-ontology

standardizing sensu definitions #1289