extend spell checker

[Clare72]

Other than spelling, OBOEdit also checked for:

• full stop at end of definition/comment
• repeated words (we probably only want this for definitions/comments)
• repeated whitespace (there doesn't seem to be a repeated punctuation check, but might be good to have this too)
• each full stop followed by space then capital letter

OBOEdit also checked that each definition had at least one reference, but this might be better to add as a custom check to the robot report rather than the spell checker.

I also found a couple of misspellings just now with oboedit that weren't in the last spellcheck report (eigth->eighth and chan->chain) - see https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/pull/1421

[gouttegd]

I have a working implementation for all those checks except the last one.

Checking that “each full stop is followed by space then capital letter” is tricky because because it’s tricky to distinguish a “full stop” (end of sentence) from all the other uses of the dot characters (e.g. in fixed locutions such as i.e., et al., .e.g; in decimal numbers; in gene names; in authors’ names, etc.), yielding a lot of false positives.

Excluding the last check, here’s what the report would now look like:

Term: segment border muscle cell (FBbt:00000483)
missing final full stop: in definition: 2012)

Term: embryonic/larval fat body (FBbt:00001704)
misspelling: in synonyms: fatbody

Term: peripodial epithelium (FBbt:00001762)
repeated words: in definition: "cells"

Term: larval PLSOh neuron (FBbt:00002620)
misspelling: in name: plsoh
misspelling: in definition: plsoh

Term: larval ASOp neuron (FBbt:00002627)
misspelling: in name: asop

Term: paraesophageal ganglion (FBbt:00002635)
misspelling: in synonyms: paraoesophageal

Term: dorsal organ (FBbt:00002655)
misspelling: in synonyms: antso

Term: dorsal organ base sensillum (FBbt:00002656)
misspelling: in synonyms: papillum

Term: dorsolateral papilla (FBbt:00002679)
misspelling: in synonyms: papillum pmod

Term: campaniform sensillum of distal group (FBbt:00002692)
misspelling: in synonyms: papillum

Term: ventral organ (FBbt:00002707)
misspelling: in synonyms: ventrales

Term: abdominal 9 dorsocaudal sensory organ PLSOh (FBbt:00002943)
misspelling: in name: plsoh

Term: abdominal 9 dorsocaudal sensory organ PLSOp (FBbt:00002944)
misspelling: in name: plsop

Term: larval basiconic sensillum of anal sense organ (FBbt:00002949)
misspelling: in synonyms: asop

Term: dorsal diaphragm (FBbt:00003171)
repeated punctuation: in definition: "??"

Term: adult fat body (FBbt:00003209)
missing final full stop: in definition: 2018)

Term: adult corpus cardiacum (FBbt:00003216)
missing final full stop: in definition: 2020)

Term: tibial depressor muscle cell (FBbt:00003322)
misspelling: in synonyms: tidm

Term: tarsal depressor muscle cell (FBbt:00003323)
misspelling: in synonyms: tadm

Term: intracoxal levator muscle cell (FBbt:00003326)
misspelling: in synonyms: trlm

Term: tibial levator muscle cell (FBbt:00003329)
misspelling: in synonyms: tilm

Term: tarsal levator muscle cell (FBbt:00003330)
misspelling: in synonyms: talm

Term: femoral reductor muscle cell (FBbt:00003332)
misspelling: in synonyms: ferm

Term: adult protocerebral bridge 1 glomerulus-fan-shaped body-lateral accessory lobe neuron (FBbt:00003635)
misspelling: in synonyms: idfp

Term: optic lobe pioneer neuron 1 (FBbt:00003704)
misspelling: in synonyms: chalv

Term: optic lobe pioneer neuron 2 (FBbt:00003705)
misspelling: in synonyms: glulv

Term: adult cervical connective (FBbt:00004019)
misspelling: in synonyms: cvcon

Term: adult ventral nerve cord (FBbt:00004052)
misspelling: in synonyms: thgng

Term: adult dorsal prothoracic nerve (FBbt:00004055)
misspelling: in synonyms: dpron

Term: adult prothoracic accessory nerve (FBbt:00004056)
misspelling: in synonyms: proan

Term: adult mesothoracic leg nerve (FBbt:00004063)
misspelling: in synonyms: mesoln

Term: direct flight muscle motor neuron (FBbt:00004065)
misspelling: in synonyms: dfmmn

Term: adult accessory mesothoracic neuropil (FBbt:00004091)
misspelling: in synonyms: amnp

Term: adult dorsal metathoracic nerve (FBbt:00004094)
misspelling: in synonyms: dmetan

Term: adult metathoracic leg nerve (FBbt:00004096)
misspelling: in synonyms: metaln

Term: adult abdominal nerve trunk (FBbt:00004099)
misspelling: in synonyms: abnt

Term: proximal rostral sensillum (FBbt:00004169)
misspelling: in synonyms: prst

Term: prothoracic trochanter campaniform sensillum Sc-8 (FBbt:00004261)
misspelling: in synonyms: trfpf

Term: prothoracic trochanter campaniform sensillum Sc3 (FBbt:00004262)
misspelling: in synonyms: trgf

Term: prothoracic trochanter campaniform sensillum Sc+5 (FBbt:00004263)
misspelling: in synonyms: trfaf

Term: prothoracic trochanter campaniform sensillum Sc13 (FBbt:00004264)
misspelling: in synonyms: trff

Term: prothoracic femoral campaniform sensillum Sc1 (FBbt:00004276)
misspelling: in synonyms: fesf

Term: prothoracic femoral campaniform sensillum Sc11 (FBbt:00004277)
misspelling: in synonyms: feff

Term: mesothoracic trochanter campaniform sensillum Sc-8 (FBbt:00004370)
misspelling: in synonyms: trfpm

Term: mesothoracic trochanter campaniform sensillum Sc3 (FBbt:00004371)
misspelling: in synonyms: trgm

Term: mesothoracic trochanter campaniform sensillum Sc+5 (FBbt:00004372)
misspelling: in synonyms: trfam

Term: mesothoracic trochanter campaniform sensillum Sc13 (FBbt:00004373)
misspelling: in synonyms: trfm

Term: mesothoracic femoral campaniform sensillum Sc1 (FBbt:00004385)
misspelling: in synonyms: fesm

Term: mesothoracic femoral campaniform sensillum Sc11 (FBbt:00004386)
misspelling: in synonyms: fefm

Term: metathoracic trochanter campaniform sensillum Sc-8 (FBbt:00004428)
misspelling: in synonyms: trfpr

Term: metathoracic trochanter campaniform sensillum Sc3 (FBbt:00004429)
misspelling: in synonyms: trgr

Term: metathoracic trochanter campaniform sensillum Sc+5 (FBbt:00004430)
misspelling: in synonyms: trfar

Term: metathoracic trochanter campaniform sensillum Sc13 (FBbt:00004431)
misspelling: in synonyms: trfr

Term: metathoracic femoral campaniform sensillum Sc1 (FBbt:00004443)
misspelling: in synonyms: fesr

Term: metathoracic femoral campaniform sensillum Sc11 (FBbt:00004444)
misspelling: in synonyms: fefr

Term: hypogynial short bristle (FBbt:00004468)
misspelling: in synonyms: trichodea

Term: female analia (FBbt:00004824)
misspelling: in synonyms: proctiger

Term: hypogynium (FBbt:00004832)
repeated spaces: in definition: 1 repeated whitespace(s)

Term: calyx of oviduct (FBbt:00004918)
misspelling: in definition: pedicels

Term: cyst progenitor cell (FBbt:00004933)
misspelling: in synonyms: cysc

Term: amnioserosa anlage in statu nascendi (FBbt:00005422)
misspelling: in synonyms: amnioser

Term: embryonic outer optic lobe (FBbt:00005661)
missing final full stop: in comment: mc11082016

Term: eyelet photoreceptor (FBbt:00005740)
misspelling: in synonyms: hbeyelet

Term: Pcd2 neuroblast (FBbt:00005865)
misspelling: in synonyms: mbnbd

Term: Pcd4 neuroblast (FBbt:00005867)
misspelling: in synonyms: mbnbb

Term: Pcd9 neuroblast (FBbt:00005879)
misspelling: in synonyms: mbnbc

Term: larval posterior lateral bundle (FBbt:00005986)
missing final full stop: in definition: 2018)

Term: Pcv9 neuroblast (FBbt:00006006)
misspelling: in synonyms: mbnba

Term: antennal segment 3 thermosensory organ (FBbt:00007334)
missing final full stop: in comment: FlyBase:FBrf0246456)

Term: vertical system neuron 1 (FBbt:00007517)
repeated words: in comment: "cells"

Term: adult prothoracic leg nerve (FBbt:00007657)
misspelling: in synonyms: proln

Term: tectulum (FBbt:00007727)
misspelling: in synonyms: tect

Term: abdominal dorso-lateral adult muscle precursor cell (FBbt:00013243)
misspelling: in synonyms: dlap

Term: dorsolateral domain of larval labial neuromere (FBbt:00015023)
misspelling: in synonyms: lbdl

Term: dorsolateral domain of larval mandibular neuromere (FBbt:00015030)
misspelling: in synonyms: mddl

Term: dorsomedial domain of larval mandibular neuromere (FBbt:00015031)
misspelling: in synonyms: mddm

Term: dorsolateral domain of larval maxillary neuromere (FBbt:00015037)
misspelling: in synonyms: mxdl

Term: ventral neurectoderm intermediate zone 2 (FBbt:00015563)
repeated words: in definition: "4"

Term: salivary gland common duct primordium (FBbt:00016005)
misspelling: in synonyms: salcd

Term: adult salivary gland anlage (FBbt:00016006)
misspelling: in synonyms: adsal

Term: amnioserosa anlage (FBbt:00017017)
misspelling: in synonyms: amnioser

Term: gorget (FBbt:00040039)
misspelling: in synonyms: vmcs

Term: superior posterior slope (FBbt:00045040)
misspelling: in synonyms: vmcpod

Term: inferior posterior slope (FBbt:00045046)
misspelling: in synonyms: vmcpov

Term: fat cell (FBbt:00046052)
misspelling: in comment: apollp

Term: intermediate zone of anterior optic tubercle (FBbt:00047045)
misspelling: in comment: aotuim
misspelling: in synonyms: aotuim

Term: adult tubercle-superior bulb neuron (FBbt:00047049)
missing final full stop: in definition: 2020)

Term: adult prothoracic anterior anterior ventral commissure (FBbt:00047133)
misspelling: in synonyms: proth

Term: wing neuropil (FBbt:00047137)
misspelling: in synonyms: wtct

Term: haltere neuropil (FBbt:00047138)
misspelling: in synonyms: htct

Term: neck neuropil (FBbt:00047173)
misspelling: in synonyms: ntct

Term: adult mesothoracic posterior anterior ventral commissure (FBbt:00047547)
repeated words: in definition: "anterior"

Term: adult mesothoracic anterior anterior ventral commissure (FBbt:00047548)
misspelling: in synonyms: mesoth

Term: adult mesothoracic anterior anterior ventral commissure (FBbt:00047548)
repeated words: in comment: "anterior"

Term: adult metathoracic anterior anterior ventral commissure (FBbt:00047550)
misspelling: in synonyms: metath

Term: adult metathoracic posterior posterior intermediate anterior commissure (FBbt:00047570)
repeated words: in definition: "posterior"

Term: adult metathoracic posterior posterior intermediate posterior commissure (FBbt:00047571)
repeated words: in definition: "posterior"

Term: adult intrinsic lateral accessory lobe neuron (FBbt:00048092)
misspelling: in synonyms: vbos

Term: vertical system-like neuron (FBbt:00048128)
misspelling: in synonyms: vslike

Term: hypandrial phragma (FBbt:00048385)
misspelling: in synonyms: fragma

Term: adult mesothoracic posterior posterior intermediate anterior commissure (FBbt:00048484)
repeated words: in definition: "posterior"

Term: adult mesothoracic posterior posterior intermediate posterior commissure (FBbt:00048485)
repeated words: in definition: "posterior"

Term: larval anterior central sensory compartment anterior medial region (FBbt:00048492)
misspelling: in synonyms: acscam

Term: larval anterior ventral sensory compartment posterior region (FBbt:00048494)
misspelling: in synonyms: avscp

Term: larval anterior central sensory compartment anterior lateral region (FBbt:00048495)
misspelling: in comment: acscal
misspelling: in synonyms: acscal

Term: larval anterior central sensory compartment posterior region (FBbt:00048496)
misspelling: in comment: acscal acscp
misspelling: in synonyms: acscal acscp

Term: larval A03x neuron (FBbt:00048632)
misspelling: in synonyms: eghb

Term: lineage MNB primary neuron (FBbt:00048864)
misspelling: in synonyms: mnbp

Term: larval A01a1 neuron (FBbt:00048981)
missing final full stop: in comment: (2021)

Term: adult lateral accessory lobe-ipsilateral nodulus 2 neuron (FBbt:00049136)
misspelling: in synonyms: crel

Term: adult lateral accessory lobe-anterior nodulus 3 neuron (FBbt:00049137)
misspelling: in synonyms: lnoa

Term: adult lateral accessory lobe-crepine-posterior and medial nodulus 3 neuron (FBbt:00049138)
misspelling: in synonyms: lcnopm lcnpm

Term: adult lateral accessory lobe-crepine-posterior nodulus 3 neuron (FBbt:00049139)
misspelling: in synonyms: crec lcnop lcnp

Term: adult bilateral superior lateral protocerebrum-asymmetrical body neuron (FBbt:00049143)
misspelling: in synonyms: abic

Term: adult superior lateral protocerebrum-asymmetrical body-fan-shaped body layer 8 neuron (FBbt:00049145)
misspelling: in synonyms: slpaf

Term: adult ellipsoid body-dorsal gall surround neuron (FBbt:00049180)
misspelling: in synonyms: ebgas

Term: dorsal protractor muscle cell (FBbt:00049189)
misspelling: in synonyms: prodo

Term: muscle cell of dorsal protractor muscle A (FBbt:00049190)
misspelling: in synonyms: prodoa

Term: muscle cell of dorsal protractor muscle B (FBbt:00049191)
misspelling: in synonyms: prodob

Term: larval longitudinal ventral posterior-lateral fascicle (FBbt:00049260)
missing final full stop: in comment: loV

Term: adult lateral horn AV1a1 neuron (FBbt:00049331)
misspelling: in synonyms: vlpn

Term: adult lateral horn AV3a1 neuron (FBbt:00049344)
missing final full stop: in definition: 2021)

Term: adult lateral horn AV4a1 neuron (FBbt:00049345)
missing final full stop: in definition: 2020)

Term: gamma-s Kenyon cell (FBbt:00049830)
misspelling: in synonyms: kcgammas

Term: gamma-t Kenyon cell (FBbt:00049833)
misspelling: in synonyms: kcgammat

Term: alpha/beta surface/core Kenyon cell (FBbt:00049838)
misspelling: in synonyms: betasc

Term: adult prothoracic chordotonal nerve (FBbt:00049893)
misspelling: in synonyms: procn

Term: neuroblast SLPpl3 (FBbt:00050006)
missing final full stop: in comment: doi:10.1101/2020.06.12.148775

Term: small unit of anterior optic tubercle (FBbt:00051217)
misspelling: in synonyms: aotusu

Term: lobula columnar neuron LC33 (FBbt:00051247)
missing final full stop: in definition: 2020)

Term: lobula columnar neuron LC27 (FBbt:00051248)
missing final full stop: in definition: 2020)

Term: larval A01a2 neuron (FBbt:00051321)
missing final full stop: in comment: (2021)

Term: gnathal neuroblast (FBbt:00051363)
missing final full stop: in definition: 2016)

Term: larval mushroom body non-intrinsic type 2 neuron (FBbt:00051367)
misspelling: in definition: mbnba

Term: larval external muscle cell (FBbt:00051428)
misspelling: in definition: connectin

Term: transient interhemispheric fibrous ring (FBbt:00051435)
missing final full stop: in comment: 2000)

Term: adult tubercle-tubercle medial zone neuron (FBbt:00051488)
misspelling: in synonyms: tutua

Term: adult tubercle-tubercle lateral zone neuron (FBbt:00051489)
misspelling: in synonyms: tutub

Term: adult brontosaraus subesophageal neuron (FBbt:00051863)
misspelling: in name: brontosaraus
misspelling: in comment: brontosaraus

Term: adult clubround subesophageal neuron (FBbt:00051869)
misspelling: in name: clubround

Term: adult doublescoop subesophageal neuron (FBbt:00051876)
misspelling: in name: doublescoop

Term: adult FMIn subesophageal neuron (FBbt:00051880)
misspelling: in name: fmin

Term: adult fudog subesophageal neuron (FBbt:00051883)
misspelling: in name: fudog

Term: adult gallinule subesophageal neuron (FBbt:00051884)
misspelling: in name: gallinule

Term: adult horntail subesophageal neuron (FBbt:00051894)
misspelling: in name: horntail

Term: adult kokopelli subesophageal neuron (FBbt:00051905)
misspelling: in name: kokopelli

Term: adult nagini subesophageal neuron (FBbt:00051918)
misspelling: in name: nagini

Term: adult pleco subesophageal neuron (FBbt:00051929)
misspelling: in name: pleco

Term: adult sundrop subesophageal neuron (FBbt:00051943)
misspelling: in name: sundrop

Term: adult tentacular subesophageal neuron (FBbt:00051945)
misspelling: in name: tentacular

Term: adult tinctoria subesophageal neuron (FBbt:00051946)
misspelling: in name: tinctoria

Term: adult tophat subesophageal neuron (FBbt:00051947)
misspelling: in name: tophat

Term: adult trogon subesophageal neuron (FBbt:00051950)
misspelling: in name: trogon

Term: adult usnea subesophageal neuron (FBbt:00051956)
misspelling: in name: usnea

Term: adult wafflecone subesophageal neuron (FBbt:00051959)
misspelling: in name: wafflecone

Term: adult octopaminergic doublesex neuron of abdominal ganglion (female) (FBbt:00052015)
missing final full stop: in definition: 2020)

Term: larval PLSOp neuron (FBbt:00052039)
misspelling: in name: plsop
misspelling: in definition: plsop

Term: larval trichoid sensillum of anal sense organ (FBbt:00052044)
misspelling: in synonyms: asoh

Term: larval ASOh neuron (FBbt:00052045)
misspelling: in name: asoh

Term: hypogynial posterodorsal pouch (FBbt:00052066)
misspelling: in synonyms: dorsodistal

Term: prothoracic tibial campaniform sensillum Sc2 (FBbt:00058049)
misspelling: in synonyms: tigdf

Term: prothoracic tibial campaniform sensillum Sc3 (FBbt:00058050)
misspelling: in synonyms: tigvf

Term: mesothoracic tibial campaniform sensillum Sc3 (FBbt:00058055)
misspelling: in synonyms: tigvm

Term: mesothoracic tibial campaniform sensillum Sc2 (FBbt:00058056)
misspelling: in synonyms: tigdm

Term: metathoracic tibial campaniform sensillum Sc3 (FBbt:00058059)
misspelling: in synonyms: tigvr

Term: metathoracic tibial campaniform sensillum Sc2 (FBbt:00058060)
misspelling: in synonyms: tigdr

Term: trochanter reductor muscle cell (FBbt:00058101)
misspelling: in synonyms: trrm

Term: femoral depressor muscle cell (FBbt:00058105)
misspelling: in synonyms: fedm

Term: tibial reductor muscle cell (FBbt:00058109)
misspelling: in synonyms: tirm

Term: tarsal reductor muscle cell (FBbt:00058113)
misspelling: in synonyms: tarm

Term: antennal trichoid sensillum at1 (FBbt:00067030)
missing final full stop: in definition: 2021)

Term: mushroom body beta' middle layer (FBbt:00100270)
misspelling: in synonyms: betam

Term: posterior cerebro-cervical fascicle (FBbt:00100344)
repeated words: in definition: "slope"

Term: neuroblast DALl1 (FBbt:00100547)
repeated words: in definition: "anterior"

Term: adult abdominal neuromere (FBbt:00110173)
misspelling: in synonyms: abgng

Term: VT1 motor neuron (FBbt:00110279)
misspelling: in synonyms: motoneuron

Term: lateral VUM motor neuron (FBbt:00110308)
misspelling: in synonyms: vumsn

Term: mFB neuron of the dopaminergic PPM3 cluster (FBbt:00110325)
missing final full stop: in comment: (2020)

Term: posterior chiasma of the central complex (FBbt:00110650)
misspelling: in synonyms: fbppl

Term: anterior chiasma of the central complex (FBbt:00110651)
misspelling: in synonyms: fbapl

Term: posterior tooth bristle of antennal segment 2 (FBbt:00110820)
misspelling: in synonyms: zahnborsten

Term: alpha/beta posterior Kenyon cell (FBbt:00110931)
misspelling: in synonyms: kcalpha

Term: gamma dorsal Kenyon cell (FBbt:00110932)
misspelling: in synonyms: gammad

Term: gamma main Kenyon cell (FBbt:00111061)
misspelling: in synonyms: gammamain

Term: larval Goro neuron (FBbt:00111240)
misspelling: in synonyms: gorogoro

Term: adult protocerebral bridge 1 glomerulus-ellipsoid body canal-gall neuron (FBbt:00111375)
missing final full stop: in comment: doi:10.1101/2020.12.08.413955)

Term: adult lateral accessory lobe-posterior slope-protocerebral bridge neuron (FBbt:00111382)
misspelling: in synonyms: lpsp lpsp

Term: adult inferior bridge-superior posterior slope-protocerebral bridge neuron (FBbt:00111383)
misspelling: in synonyms: ibsps ibspsp ibspsp

Term: protocerebral bridge 1 glomerulus-fan-shaped body-nodulus 2 dorsal domain neuron (FBbt:00111390)
misspelling: in comment: pfnd
misspelling: in synonyms: pfnd

Term: protocerebral bridge 1 glomerulus-fan-shaped body-nodulus 3 anterior domain neuron (FBbt:00111396)
misspelling: in comment: pfna
misspelling: in synonyms: pfna

Term: protocerebral bridge 1 glomerulus-fan-shaped body-nodulus 3 posterior domain neuron (FBbt:00111404)
misspelling: in comment: pfnp
misspelling: in synonyms: pfnp

Term: adult ellipsoid body-protocerebral bridge glomerulus 9-gall tip neuron (FBbt:00111423)
misspelling: in synonyms: epgt

Term: protocerebral bridge 1 glomerulus-fan-shaped body layer 2-lateral accessory lobe-crepine neuron (FBbt:00111433)
misspelling: in synonyms: lcre

Term: protocerebral bridge 1 glomerulus-fan-shaped body-nodulus 2 ventral domain neuron (FBbt:00111512)
misspelling: in comment: pfnv
misspelling: in synonyms: pfnv

Term: protocerebral bridge 1 glomerulus-fan-shaped body-nodulus 3 medial domain neuron (FBbt:00111513)
misspelling: in comment: pfnm
misspelling: in synonyms: pfnm

Term: adult superior posterior slope-protocerebral bridge neuron (FBbt:00111514)
misspelling: in synonyms: spsi spsp

Term: median neuroblast MNB interneuron (FBbt:00111616)
misspelling: in synonyms: mnbp

Term: larval antennal lobe multiglomerular projection neuron D (FBbt:00111720)
repeated words: in definition: "takes"

Term: adult superior posterior slope-bulb-tubercle neuron (FBbt:20000045)
misspelling: in definition: aotus

[Clare72]

looks good! The oboedit report always had a lot of false positives, so it was sometimes hard to spot actual problems, so maybe it is not worth having the full stop, space, capital check. I don't see the double space in the 'hypogynium' definition - is this something you added for testing (or maybe an old version of FBbt)?

[gouttegd]

I don't see the double space in the 'hypogynium' definition - is this something you added for testing (or maybe an old version of FBbt)?

Yes, it’s fixed in the current -edit file (apparently you fixed it in April), sorry about that.