Inappropriate capitalizations

[cmungall]

See #12540 and cmungall/capital-offence#1

Pathway

• GO:0033499 ! galactose catabolic process via UDP-galactose [SYNONYM: "galactose breakdown via UDP-galactose" (exact)] [SYNONYM: "galactose catabolism via UDP-galactose" (exact)] [SYNONYM: "galactose degradation via UDP-galactose" (exact)] [SYNONYM: "Leloir Pathway " (related)]
• GO:0061688 ! glycolytic process via Entner-Doudoroff Pathway

Complex

• GO:0000813 ! ESCRT I complex [SYNONYM: "Endosomal Sorting Complex Required for Transport" (broad)]
• GO:0000814 ! ESCRT II complex [SYNONYM: "Endosomal Sorting Complex Required for Transport" (broad)]
• GO:0000815 ! ESCRT III complex [SYNONYM: "Endosomal Sorting Complex Required for Transport" (broad)]
• GO:0030964 ! NADH dehydrogenase complex [SYNONYM: " Complex I" (exact)] [SYNONYM: "NADH dehydrogenase complex (plastoquinone)" (narrow)] [SYNONYM: "NADH dehydrogenase complex (quinone)" (narrow)] [SYNONYM: "NADH dehydrogenase complex (ubiquinone)" (narrow)] [SYNONYM: "NADH:plastoquinone reductase complex" (narrow)] [SYNONYM: "plastid NADH dehydrogenase complex (plastoquinone)" (narrow)]
• GO:1990203 ! MdtBC Complex [SYNONYM: "multidrug efflux pump MdtBC" (exact)]
• GO:1990469 ! Rhino-Deadlock-Cutoff Complex [SYNONYM: "RDC complex" (exact)] [SYNONYM: "rhi-del-cuff complex" (exact)]

Greek alphabet

• GO:0086096 ! adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process [SYNONYM: "cardiac adrenergic receptor signaling pathway via inhibition of adenylate cyclase activity" (exact)] [SYNONYM: "G-inhibitory-coupled Beta 2AR signaling pathway involved in heart process" (exact)] [SYNONYM: "Gi-coupled adrenergic receptor signaling pathway involved in heart process" (exact)] [SYNONYM: "Gi-coupled Beta 2-AR signaling pathway involved in heart process" (exact)]
• GO:1990711 ! Beta -catenin-ICAT complex [SYNONYM: "CTNNB1-CTNNBIP1 complex" (exact)]

We use "beta-catenin" in other places

• GO:0032093 ! SAM domain binding [SYNONYM: "Sterile Alpha Motif domain binding" (exact)]

this should be "sterile alpha morif"

Note I do not include a report for Delta, as we have so many, this is probably OK nomenclature

Polymerase

• GO:0061427 ! negative regulation of ceramide biosynthetic process by negative regulation of transcription from RNA Polymerase II promoter
• GO:1990113 ! RNA Polymerase I assembly [SYNONYM: "DNA-directed RNA polymerase I complex assembly" (exact)] [SYNONYM: "RNA Polymerase I complex assembly" (exact)]
• GO:1990114 ! RNA Polymerase II core complex assembly [SYNONYM: "DNA-directed RNA polymerase II, core complex assembly" (exact)] [SYNONYM: "RNA Polymerase II assembly" (broad)]
• GO:1990115 ! RNA Polymerase III assembly [SYNONYM: "DNA-directed RNA polymerase III complex assembly" (exact)] [SYNONYM: "RNA Polymerase III complex assembly" (exact)]

we tend to use "polymerase" (even though there is a protein name based argument for capitalization)

Thyroid

• GO:1904400 ! response to Thyroid stimulating hormone
• GO:1904401 ! cellular response to Thyroid stimulating hormone

We normally use "thyroid-stimulating hormone"

Group

• GO:0000372 ! Group I intron splicing [SYNONYM: "mRNA splicing" (related)]
• GO:0000373 ! Group II intron splicing [SYNONYM: "mRNA splicing" (related)]
• GO:0000374 ! Group III intron splicing [SYNONYM: "mRNA splicing" (related)]
• GO:0001639 ! PLC activating G-protein coupled glutamate receptor activity [SYNONYM: " Group I metabotropic glutamate receptor" (related)] [SYNONYM: "group I metabotropic glutamate receptor activity" (related)] [SYNONYM: "phospholipase C activating metabotropic glutamate receptor activity" (exact)] [SYNONYM: "PLC activating metabotropic glutamate receptor activity" (exact)]
• GO:0031519 ! PcG protein complex [SYNONYM: "Polycomb Group protein complex" (exact)]

it is more common for us to say "group I intron". See also the form here https://en.wikipedia.org/wiki/Group_I_catalytic_intron#Catalysis

Intermediate

• GO:0022894 ! Intermediate conductance calcium-activated potassium channel activity [SYNONYM: "IK calcium-activated potassium channel activity" (exact)] [SYNONYM: "IK KCa channels" (exact)] [SYNONYM: "intermdiate conductance KCa channels" (exact)]

Regulation, Inhibition, Transport

• GO:0043405 ! regulation of MAP kinase activity [SYNONYM: " Regulation of MAPK activity" (exact)] [SYNONYM: "regulation of mitogen activated protein kinase activity" (exact)] [SYNONYM: "regulation of mitogen-activated protein kinase activity" (exact)]
• GO:0039548 ! suppression by virus of host IRF3 activity [SYNONYM: "inhibition of host IRF3 by virus" (exact)] [SYNONYM: " Inhibition of IRF3-dependent antiviral response" (broad)] [SYNONYM: "suppression by virus of host interferon regulatory factor 3" (exact)]
• GO:0039554 ! suppression by virus of host MDA-5 activity [SYNONYM: "inhibition of host IFIH1/MDA5 by virus" (related)] [SYNONYM: " Inhibition of host MDA5 by virus" (exact)]
• GO:0039563 ! suppression by virus of host STAT1 activity [SYNONYM: "inhibition by virus of host STAT1 activity" (narrow)] [SYNONYM: " Inhibition of host STAT1 by virus" (narrow)]
• GO:0039564 ! suppression by virus of host STAT2 activity [SYNONYM: "inhibition by virus of host STAT2 activity" (narrow)] [SYNONYM: " Inhibition of host STAT2 by virus" (exact)]
• GO:0039611 ! suppression by virus of host translation initiation factor activity [SYNONYM: "inactivation of eIF2 activity" (narrow)] [SYNONYM: "inhibition of activity of host translation initiation factor" (exact)] [SYNONYM: " Inhibition of host translation factors by virus" (broad)] [SYNONYM: "suppression by virus of host EIF-4E activity" (exact)]
• GO:0000813 ! ESCRT I complex [SYNONYM: "Endosomal Sorting Complex Required for Transport " (broad)]
• GO:0000814 ! ESCRT II complex [SYNONYM: "Endosomal Sorting Complex Required for Transport " (broad)]
• GO:0000815 ! ESCRT III complex [SYNONYM: "Endosomal Sorting Complex Required for Transport " (broad)]

Chemical names

There are a lot of these. There is an argument that drugs are proper names and can be capitalized, but it's still better to be consistent

• GO:0052598 ! histamine oxidase activity [SYNONYM: "1H- Imidazole -4-ethanamine oxidase activity" (exact)] [SYNONYM: "1H- Imidazole -4-ethanamine:oxygen oxidoreductase (deaminating) activity" (exact)] [SYNONYM: "histamine:oxygen oxidoreductase (deaminating) activity" (exact)]

Taxon common names

The Linnaen name is always capitalized. However, common names should not be. Offences:

• GO:0009275 ! Gram-positive-bacterium-type cell wall [SYNONYM: "20-80nm peptidoglycan-based cell wall" (exact)] [SYNONYM: "cell wall of Gram-positive Bacteria " (exact)]

Proper names that should be capitalized

Warburg

• GO:0004129 ! cytochrome-c oxidase activity [SYNONYM: "aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "caa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "cytochrome a3 activity" (narrow)] [SYNONYM: "cytochrome aa3 activity" (narrow)] [SYNONYM: "cytochrome c oxidase activity" (exact)] [SYNONYM: "cytochrome oxidase activity" (related)] [SYNONYM: "ferrocytochrome c oxidase" (narrow)] [SYNONYM: "ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "indophenol oxidase" (narrow)] [SYNONYM: "indophenolase" (narrow)] [SYNONYM: "NADH cytochrome c oxidase" (exact)] [SYNONYM: " warburg 's respiratory enzyme activity" (related)]

plus many derivative terms:

• GO:1904959 ! regulation of cytochrome-c oxidase activity [SYNONYM: "regulation of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "regulation of ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "regulation of caa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "regulation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "regulation of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "regulation of cytochrome a3 activity" (narrow)] [SYNONYM: "regulation of cytochrome aa3 activity" (narrow)] [SYNONYM: "regulation of cytochrome c oxidase activity" (exact)] [SYNONYM: "regulation of cytochrome oxidase activity" (related)] [SYNONYM: "regulation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "regulation of ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "regulation of indophenol oxidase" (narrow)] [SYNONYM: "regulation of indophenolase" (narrow)] [SYNONYM: "regulation of NADH cytochrome c oxidase" (exact)] [SYNONYM: "regulation of warburg 's respiratory enzyme activity" (related)] * GO:1904960 ! positive regulation of cytochrome-c oxidase activity [SYNONYM: "activation of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "activatio
  n of ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "activation of caa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "activation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "activatio
  n of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "activation of cytochrome a3 activity" (narrow)] [SYNONYM: "activation of cytochrome aa3 activity" (narrow)] [SYNONYM:
  "activation of cytochrome c oxidase activity" (narrow)] [SYNONYM: "activation of cytochrome oxidase activity" (related)] [SYNONYM: "activation of cytochrome-c oxidase activity" (narrow)] [SYNONYM: "a
  ctivation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "activation of ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "activation of indophenol oxidase" (narrow)] [SYNONYM: "activati
  on of indophenolase" (narrow)] [SYNONYM: "activation of NADH cytochrome c oxidase" (narrow)] [SYNONYM: "activation of warburg 's respiratory enzyme activity" (related)] [SYNONYM: "positive regula
  tion of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "positive regulation of ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "positive regulation of caa3-type cytochrome c oxidase" (narrow)]
  [SYNONYM: "positive regulation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "positive regulation of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "positive reg
  ulation of cytochrome a3 activity" (narrow)] [SYNONYM: "positive regulation of cytochrome aa3 activity" (narrow)] [SYNONYM: "positive regulation of cytochrome c oxidase activity" (exact)] [SYNONYM: "p
  ositive regulation of cytochrome oxidase activity" (related)] [SYNONYM: "positive regulation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "positive regulation of ferrocytochrome-c:oxygen oxidored
  uctase" (narrow)] [SYNONYM: "positive regulation of indophenol oxidase" (narrow)] [SYNONYM: "positive regulation of indophenolase" (narrow)] [SYNONYM: "positive regulation of NADH cytochrome c oxidase
  " (exact)] [SYNONYM: "positive regulation of warburg 's respiratory enzyme activity" (related)] [SYNONYM: "up regulation of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up regulation of ba
  3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up regulation of caa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up regulation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up regulat
  ion of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "up regulation of cytochrome a3 activity" (narrow)] [SYNONYM: "up regulation of cytochrome aa3 activity" (narrow)] [
  SYNONYM: "up regulation of cytochrome c oxidase activity" (exact)] [SYNONYM: "up regulation of cytochrome oxidase activity" (related)] [SYNONYM: "up regulation of cytochrome-c oxidase activity" (exact
  )] [SYNONYM: "up regulation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "up regulation of ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "up regulation of indophenol oxidase" (narr
  ow)] [SYNONYM: "up regulation of indophenolase" (narrow)] [SYNONYM: "up regulation of NADH cytochrome c oxidase" (exact)] [SYNONYM: "up regulation of warburg 's respiratory enzyme activity" (rela
  ted)] [SYNONYM: "up-regulation of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up-regulation of ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up-regulation of caa3-type cytochrome c oxida
  se" (narrow)] [SYNONYM: "up-regulation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "up-regulation of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "up-regulat
  ion of cytochrome a3 activity" (narrow)] [SYNONYM: "up-regulation of cytochrome aa3 activity" (narrow)] [SYNONYM: "up-regulation of cytochrome c oxidase activity" (exact)] [SYNONYM: "up-regulation of
  cytochrome oxidase activity" (related)] [SYNONYM: "up-regulation of cytochrome-c oxidase activity" (exact)] [SYNONYM: "up-regulation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "up-regulation of
  ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "up-regulation of indophenol oxidase" (narrow)] [SYNONYM: "up-regulation of indophenolase" (narrow)] [SYNONYM: "up-regulation of NADH cyto
  chrome c oxidase" (exact)] [SYNONYM: "up-regulation of warburg 's respiratory enzyme activity" (related)] [SYNONYM: "upregulation of aa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "upregulati
  on of ba3-type cytochrome c oxidase" (narrow)] [SYNONYM: "upregulation of caa3-type cytochrome c oxidase" (narrow)] [SYNONYM: "upregulation of cbb3-type cytochrome c oxidase" (narrow)] [SYNONYM: "upregulation of complex IV (mitochondrial electron transport) activity" (related)] [SYNONYM: "upregulation of cytochrome a3 activity" (narrow)] [SYNONYM: "upregulation of cytochrome aa3 activity" (narrow)] [SYNONYM: "upregulation of cytochrome c oxidase activity" (exact)] [SYNONYM: "upregulation of cytochrome oxidase activity" (related)] [SYNONYM: "upregulation of cytochrome-c oxidase activity" (exact)] [SYNONYM: "upregulation of ferrocytochrome c oxidase" (narrow)] [SYNONYM: "upregulation of ferrocytochrome-c:oxygen oxidoreductase" (narrow)] [SYNONYM: "upregulation of indophenol oxidase" (narrow)] [SYNONYM: "upregulation of indophenolase" (narrow)] [SYNONYM: "upregulation of NADH cytochrome c oxidase" (exact)] [SYNONYM: "upregulation of warburg 's respiratory enzyme activity" (related)]

[mcourtot]

as for #12540 : those will be automatically fixed by script and are mentioned here just for tracking, correct?

[cmungall]

If the eds approve

[mcourtot]

Ok - will put on agenda for next call.
http:https://wiki.geneontology.org/index.php/Ontology_meeting_2016-07-21

[pgaudet]

@dougli1sqrd we need a check for this.

[cmungall]

I'd like to add a spellcheck command to robot that would also check for inappropriate capitalization/case:

ontodev/robot#784

We can use this ticket as a test. This isn't a super-high priority check however