Semantic resources project/MouseModels/Missing alleles

This query compares the "allele" names occurring in strain names (from the MGI strain name report) to the "allele" name occuring in the MGI phenotypic alleles report, and reports on names present in the former but not in the latter. prefix :  select distinct ?name ?allele where { graph  {   ?s :hasStrainName ?name. ?s :hasAllele ?allele. optional { ?a :hasAlleleSymbol ?allele. ?a :hasMgiId ?m. }   filter ( !bound(?a) ) } }

Query results follow, with commentary:

My parser can't deal with this one, because of the two hyphens: B10.A-H2&lt;h4>/(4R)SgDvEg-Sh3pxd2b&lt;nee>   (4R)SgDvEg-Sh3pxd2b&lt;nee> One wouldn't expect the modifications to be listed in the phenotypic alleles report: B6.Cg-(D10Mit126-D10Mit38) Itgb2&lt;tm1Bay> (D10Mit126-D10Mit38) B6.Cg-(D10Mit75-D10Mit271) Itgb2&lt;tm1Bay> (D10Mit75-D10Mit271) C.B10-(D11Mit2-D11Mit29)                (D11Mit2-D11Mit29) B6.C3-(D13Mit147-D13Mit77)              (D13Mit147-D13Mit77) B10.BXSB-(D13Mit3-D13Mit78)             (D13Mit3-D13Mit78) B10.BXSB-(D13Mit3-D13Mit78) Yaa         (D13Mit3-D13Mit78) C.D2-(D15Mit12-D15Mit267)               (D15Mit12-D15Mit267) C.D2-(D15Mit267-D15Mit41)               (D15Mit267-D15Mit41) B6.CAST-(D17Mit19-D17Mit91)             (D17Mit19-D17Mit91) A.B6-(D17Mit29-D17Mit11)                (D17Mit29-D17Mit11) B6.MSM-(D17Mit58-D17Mit168)             (D17Mit58-D17Mit168) FVB.B6-(D18Mit129-D18Mit25)             (D18Mit129-D18Mit25) FVB.B6-(D18Mit141-D18Mit25)             (D18Mit141-D18Mit25) FVB.B6-(D18Mit186-D18Mit4)              (D18Mit186-D18Mit4) B6.D2-(D1Mit145-D1Mit17)                (D1Mit145-D1Mit17) B6.C3-(D1Mit282-D1Mit406)               (D1Mit282-D1Mit406) NOD.B6-(D1Mit369-D1Mit155)(D6Mit105-D6Mit135) (D1Mit369-D1Mit155)(D6Mit105-D6Mit135) B6.BR-(D1Mit5-D1Mit17)                  (D1Mit5-D1Mit17) A.B6-(D1Mit60-D1Mit217)                 (D1Mit60-D1Mit217) B10.A-(D1Mit65-D1Mit334)                (D1Mit65-D1Mit334) TSOD.C-(D2Mit157-D2Mit92)               (D2Mit157-D2Mit92) AKR.B6-(D4Mit13-D4Mit54)                (D4Mit13-D4Mit54) NOD.B6-(D4Mit193-D4Mit17)               (D4Mit193-D4Mit17) B6.NZB-(D4Mit193-D4Mit33)               (D4Mit193-D4Mit33) B6.D2-(D4Mit37-tel)                     (D4Mit37-tel) A.B6-(D5Mit200-D5Mit10)                 (D5Mit200-D5Mit10) B6.SJL-(D5Mit302-D5Mit307)              (D5Mit302-D5Mit307) D2.B6-(D5Mit345-D5Mit403)               (D5Mit345-D5Mit403) B6.D2-(D5Mit75-D5Mit403)                (D5Mit75-D5Mit403) NOD.B6-(D6Mit105-D6Mit135)              (D6Mit105-D6Mit135) B6.NOD-(D6Mit259-D6Mit304)              (D6Mit259-D6Mit304) B6.C3-(D6Mit93-D6Mit150)                (D6Mit93-D6Mit150) B6.C3-(D8Mit4-D8Mit167)                 (D8Mit4-D8Mit167) Need to investigate: BTBR.SPR-(H19-Cdkn1c)                   (H19-Cdkn1c) B6.CAST-(H19-Cdkn1c)                    (H19-Cdkn1c) C.D2-(Hba-a2-Es3)                       (Hba-a2-Es3) "+" looks syntactically like an allele, but isn't really: C57BL/6J-Pldn&lt;pa> Fbn1&lt;Tsk> a/Pldn&lt;pa> + a + BKS.Cg-Dock7&lt;m> +/+ Lepr&lt;db> Grid2&lt;ho-12J> + CHMU/Le-Foxc1&lt;ch> +/+ Muted&lt;mu>         + C3H-T tf/t&lt;w71> +                       + C57BL/6J-Pldn&lt;pa> +/+ Fbn1&lt;Tsk>         + LDJ/Le-Grem1&lt;ld-J> + a/ + Atrn&lt;mg> a    + BKS.Cg-Dock7&lt;m> +/+ Lepr&lt;db>            + C3H/HeSn-T tf/+ tf                      + C57BL/10Nimr-+/Pax6&lt;Sey-H>              + Need to investigate: B6.NOD-Aec1&lt;NOD/ShiLt> Aec2&lt;NOD/ShiLt>  Aec1&lt;NOD/ShiLt> B6.NOD-Aec1&lt;NOD/ShiLt> Aec2&lt;NOD/ShiLt>  Aec2&lt;NOD/ShiLt> D2.B6-Alcw2&lt;C57BL/6J>                   Alcw2&lt;C57BL/6J> B6.129P2-Apoe&lt;tm1Unc>-T&lt;8J>             Apoe&lt;tm1Unc>-T&lt;8J> DBA/2-B2m&lt;b>                            B2m&lt;b> B6.CAST-Bmd1b&lt;CAST/EiJ>                 Bmd1b&lt;CAST/EiJ> NFS.SL-Bomb1&lt;SL/Kh>                     Bomb1&lt;SL/Kh> NFS/N-Bxv1                              Bxv1 FVB.B6-CD151&lt;tm1Lka>                    CD151&lt;tm1Lka> B6.129P2-CD27&lt;tm1Jbo>                   CD27&lt;tm1Jbo> PERU-COPPOCK                            COPPOCK Not expected in phenotypic allele report (i.e. these are not really problems): C57BL/6JIco-Chr 17&lt;DBA/2NCrl>           Chr 17&lt;DBA/2NCrl> C57BL/6J-Chr 17&lt;MSM/Ms>                 Chr 17&lt;MSM/Ms> 129-Eif2s2&lt;Gt(XH413)Byg> Chr 19&lt;MOLF/Ei> Chr 19&lt;MOLF/Ei> 129S1.C3-A&lt;y>/A&lt;w> Chr 19&lt;MOLF/Ei>      Chr 19&lt;MOLF/Ei> 129-Raly&lt;Gt(RST374)Byg> Chr 19&lt;MOLF/Ei> Chr 19&lt;MOLF/Ei> 129/Sv-Tg(ACTB-A)1Jahe Chr 19&lt;MOLF/Ei>  Chr 19&lt;MOLF/Ei> 129S1.C3-A&lt;vy>/A&lt;w> Chr 19&lt;MOLF/Ei>     Chr 19&lt;MOLF/Ei> C57BL/6-Chr 19&lt;PWK> tmgc36              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> tmgc41              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> tmgc52              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> tmgc55              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> Tmgc19              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> Tmgc21              Chr 19&lt;PWK> C57BL/6-Chr 19&lt;PWK> Edn3&lt;tmgc48>        Chr 19&lt;PWK> C57BL/6JIco-Chr 6&lt;DBA/2NCrl>            Chr 6&lt;DBA/2NCrl> C57BL/6J-Chr 7&lt;129S1/SvImJ>             Chr 7&lt;129S1/SvImJ> AKR-Chr X/Y&lt;dom>                        Chr X C57BL/6JEi-Chr Y&lt;AKR>                    Chr Y&lt;AKR> C57BL/6-Chr Y&lt;AKR>                      Chr Y&lt;AKR> B6.Cg-Map3k4&lt;tm1Flv> Chr Y&lt;AKR>         Chr Y&lt;AKR> C57BL/6JEi-Chr Y&lt;BUB>                   Chr Y&lt;BUB> C57BL/6JEi-Chr Y&lt;CZECHII>               Chr Y&lt;CZECHII> C57BL/6-Chr Y&lt;FVB>                      Chr Y&lt;FVB> C57BL/6JEi-Chr Y&lt;ORB>                   Chr Y&lt;ORB> C57BL/6JEi-Chr Y&lt;PL/J>                  Chr Y&lt;PL/J> B6.129-Chr Y&lt;POS> Rsxr&lt;129S1/Sv>        Chr Y&lt;POS> C57BL/6J-Chr Y&lt;POS>                     Chr Y&lt;POS> FVB-Tg(Wap-HRAS)69Lln Chr Y&lt;SJL>        Chr Y&lt;SJL> C57BL/6-Chr Y&lt;SJL>                      Chr Y&lt;SJL> C57BL/6-Chr Y&lt;TIR>                      Chr Y&lt;TIR> C57BL/6-Chr Y&lt;dom>                      Chr Y&lt;dom> C57BL/6-Chr Y&lt;met>                      Chr Y&lt;met> Need to investigate: MRL.Cg-Coro1a&lt;C57BL/6Scr> Fas&lt;lpr>      Coro1a&lt;C57BL/6Scr> B6.MRL-Coro1a&lt;MRL/MpScr> Fas&lt;lpr>       Coro1a&lt;MRL/MpScr> I'm probably confused about the following; in something of the form x/y I treat x and y as alleles, as sometimes I have to, but in the phenotypic alleles report some of these are indexed as x/y: B6.129-Cyp1a1/Cyp1a2&lt;tm1.1Bra>          Cyp1a1 B6.129-Cyp1a2/Cyp1a1&lt;tm2Dwn>            Cyp1a1&lt;tm2Dwn> B6.Cg-Cyp1a2/Cyp1a1&lt;tm2Dwn> Tg(CYP1A1,CYP1A2)1Dwn Cyp1a1&lt;tm2Dwn> B6.129-Cyp1a2/Cyp1a1&lt;tm2Dwn>            Cyp1a2 B6.Cg-Cyp1a2/Cyp1a1&lt;tm2Dwn> Tg(CYP1A1,CYP1A2)1Dwn Cyp1a2 B6.129-Cyp1a1/Cyp1a2&lt;tm1.1Bra>          Cyp1a2&lt;tm1.1Bra> Need to investigate: B6.129P2-Dp(17Abcg1-Cbs1)1Yah           Dp(17Abcg1-Cbs1)1Yah The following has idiosyncratic syntax - 'Ei' must be a lab code, and the suffix -XO is simply ad hoc: FVB/NJ-Tg(Tyr)3412ARpw/Ei-XO            Ei-XO Need to investigate: NFS-Emv12                               Emv12 B6.129-Esam1&lt;tm1Dvst>                   Esam1&lt;tm1Dvst> B6.129S1-Etv6&lt;tm1(Runx1)Haho>           Etv6&lt;tm1(Runx1)Haho> B6.129S2-Evx2/Hoxd13&lt;tm4(cre)Ddu> Del(2Hoxd4-Hoxd13)28Ddu Evx2 More cases of multiple hyphens leading to a misparse: MRL-Fas&lt;lpr>.129P2(B6)-B2m&lt;tm1Unc>      Fas&lt;lpr>.129P2(B6)-B2m&lt;tm1Unc> B6.CAST-Gpi1&lt;a>.Cg-Hba&lt;th-J>            Gpi1&lt;a>.Cg-Hba&lt;th-J> Need to investigate: B10.LP-H13&lt;b> A&lt;w>                      H13&lt;b> B6.C-H15&lt;c> H16&lt;c> H21&lt;c>               H15&lt;c> B6.C-H15&lt;c> H16&lt;c> H21&lt;c>               H16&lt;c> This one is a mistake; the alleles report has it written DMa (capital M): B6.129S4-H2-Dma&lt;tm1Luc>                 H2-Dma&lt;tm1Luc> Need to investigate: B6.KB2-H2-M1                            H2-M1 C.D2-H2-Q7 Pstpip2&lt;cmo>                 H2-Q7 C57BL/6Fla-H2-T18                       H2-T18 B6.C-H15&lt;c> H16&lt;c> H21&lt;c>               H21&lt;c> B6.KB2-H2&lt;b5>                           H2&lt;b5> B10.LP-H3&lt;b>                            H3&lt;b> B6By.C-H8&lt;c>                            H8&lt;c> B6.129X1-Hcst/Tyrobp&lt;tm1Ttk>            Hcst B6.129S2-Evx2/Hoxd13&lt;tm4(cre)Ddu> Del(2Hoxd4-Hoxd13)28Ddu Hoxd13&lt;tm4(cre)Ddu> 129S7/SvEvBrd-Hprt&lt;+>                   Hprt&lt;+> B6.NOD-Idd3&lt;NOD> Idd10&lt;NOD/Lt>          Idd10&lt;NOD/Lt> B6.NOD-Idd13                            Idd13 B6.NOD-Idd3&lt;NOD/ShiLt> Idd5&lt;NOD/ShiLt>  Idd3&lt;NOD/ShiLt> B6.NOD-Idd3&lt;NOD> Idd10&lt;NOD/Lt>          Idd3&lt;NOD> B6.NOD-Idd4                             Idd4 NOD.B10Sn-Idd5.1&lt;C57BL/10SnJ>/R46MrkTacJ Idd5.1&lt;C57BL/10SnJ> NOD.B10Sn-Idd5&lt;C57BL/10SnJ>/R193MrkTacJ Idd5&lt;C57BL/10SnJ> B6.NOD-Idd3&lt;NOD/ShiLt> Idd5&lt;NOD/ShiLt>  Idd5&lt;NOD/ShiLt> B6.NOD-Idd6                             Idd6 NOD.C3-Idd6.2&lt;C3H/HeJ>                  Idd6.2&lt;C3H/HeJ> NOD.C3-Idd6&lt;C3H/HeJ>                    Idd6&lt;C3H/HeJ> NOD.B10-Idd9.1&lt;C57BL/10SnJ>             Idd9.1&lt;C57BL/10SnJ> NOD.B10-Idd9.2&lt;C57BL/10SnJ>             Idd9.2&lt;C57BL/10SnJ> NOD.B10-Idd9.3&lt;C57BL/10SnJ>             Idd9.3&lt;C57BL/10SnJ> NOD.B10-Idd9&lt;C57BL/10SnJ>               Idd9&lt;C57BL/10SnJ> B6.C3H-Igf1sl2&lt;C3H/HeJ>                 Igf1sl2&lt;C3H/HeJ> C.129P2/OlaHsd-Il4/Il13&lt;tm3Anjm>        Il13&lt;tm3Anjm> C.Cg-Il4/Il13&lt;tm3Anjm>                  Il13&lt;tm3Anjm> C.129P2/OlaHsd-Il4/Il13&lt;tm3Anjm>        Il4 C.Cg-Il4/Il13&lt;tm3Anjm>                  Il4 B6.MOLF-Slc11a1&lt;r> Ity3&lt;MOLF/Ei>        Ity3&lt;MOLF/Ei> Another syntax that doesn't follow nomenclature rules: MRL/MpJ-Fas&lt;lpr>/J-ggld                 J-ggld Need to investigate: 129S1/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+> Mc1r&lt;e> Kitl&lt;+> 129S2/SvPas-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+>      Kitl&lt;+> B6.129S2(D2)-Krt1-17&lt;tm1Cou>            Krt1-17&lt;tm1Cou> MRL.Cg-Lmb1&lt;C57BL/6Scr> Fas&lt;lpr>        Lmb1&lt;C57BL/6Scr> B6.MRL-Lmb1&lt;MRL/MpScr> Fas&lt;lpr>         Lmb1&lt;MRL/MpScr> B6.MRL-Lmb2&lt;MRL/MpScr> Fas&lt;lpr>         Lmb2&lt;MRL/MpScr> B6.MRL-Lmb4&lt;MRL/MpScr> Fas&lt;lpr>         Lmb4&lt;MRL/MpScr> C57BL/6-Lta/Tnf&lt;tm1Jods>                Lta C57BL/6J-Lta/Tnf&lt;tm1Jods>               Lta B6.Cg-Ltb/Tnf/Lta&lt;tm1Dvk>               Ltb CPB-MO                                  MO B6.Cg-Mapk12&lt;tm1Shir>                    Mapk12&lt;tm1Shir> B6.CAST-Mob5&lt;CAST/Ei>                   Mob5&lt;CAST/Ei> B6.CAST-Mob6&lt;CAST/Ei>                   Mob6&lt;CAST/Ei> D2.B6-Mop2&lt;C57BL/6J>                    Mop2&lt;C57BL/6J> B6.D2-Mop2&lt;DBA/2J>                      Mop2&lt;DBA/2J> FVB/N-Morc&lt;Tg(Tyr)1Az>                  Morc&lt;Tg(Tyr)1Az> C.A2G-Mx1                               Mx1 BALB.A2G-Mx1                            Mx1 B6.Cg-Nba2&lt;NZB> Tlr7&lt;tm1Aki> Yaa        Nba2&lt;NZB> TSOD.C-Nidd5&lt;BALB/cA>                   Nidd5&lt;BALB/cA> C.TSOD-Nidd5&lt;TSOD>                      Nidd5&lt;TSOD> TSOD.C-Nidd6&lt;BALB/cA>                   Nidd6&lt;BALB/cA> 129S/SvEv-Oca2&lt;+> Tyr&lt;+>                Oca2&lt;+> 129S1/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+> Mc1r&lt;e> Oca2&lt;+> 129/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;Sl-J>        Oca2&lt;+> 129S1/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;Sl>        Oca2&lt;+> 129S2/SvPas-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+>      Oca2&lt;+> FVB/N-Ods                               Ods C3HeB/FeJ-Pax6&lt;GsfAey11>                Pax6&lt;GsfAey11> B6.129-Pirt1&lt;tm1Xzd>                    Pirt1&lt;tm1Xzd> B6.C-Plgr1&lt;BALB/cJ>                     Plgr1&lt;BALB/cJ> B6.C3Sn-Psp&lt;a> A&lt;hvy>                   Psp&lt;a> C57BL/6J-Psp&lt;a>/Psp&lt;b> A&lt;hvy>/a         Psp&lt;a> C57BL/6J-Psp&lt;a>/Psp&lt;b> A&lt;hvy>/a         Psp&lt;b> DKI-R                                   R NOD.B10Sn-Idd5&lt;C57BL/10SnJ>/R193MrkTacJ  R193MrkTacJ NOD.B10Sn-Idd5.1&lt;C57BL/10SnJ>/R46MrkTacJ R46MrkTacJ C57BL/6JEi-Rb(11.16)2H                  Rb(11.16)2H AKR-Rb(6.15)1Ald                        Rb(6.15)1Ald CByJ.RBF-Rb(8.12)5Bnr                   Rb(8.12)5Bnr B6.129S6-Rbp2&lt;tm1.1Kael>                Rbp2&lt;tm1.1Kael> CPB-S                                   S D2.B6-Scpro6&lt;C57BL/6J>                   Scpro6&lt;C57BL/6J> B6.D2-Scpro6&lt;DBA/2J>                    Scpro6&lt;DBA/2J> 129.B6-Ses1a&lt;C57BL/6J>                  Ses1a&lt;C57BL/6J> 129.B6-Ses1b&lt;C57BL/6J>                  Ses1b&lt;C57BL/6J> B10.L-Slc11a1&lt;Lsh>                      Slc11a1&lt;Lsh> B6.129-Sle16&lt;129S6/SvEvTac>             Sle16&lt;129S6/SvEvTac> BTBR.B6-T2dm2&lt;C57BL/6J>                 T2dm2&lt;C57BL/6J> CPB-TK                                  TK B6.Cg-Tg(Actb-TNFRSF6B)754Jwu            Tg(Actb-TNFRSF6B)754Jwu C57BL/6-Tg(Pcp2-Fmr1*)1Dln              Tg(Pcp2-Fmr1*)1Dln FVB-Tg(Pomc-Cre)5Brn                    Tg(Pomc-Cre)5Brn B6.Cg-Il4ra&lt;tm2Tch> Tg(Scgb1a1-rtTA,tetO-IL13)1Eli Tg(Scgb1a1-rtTA,tetO-IL13)1Eli B6.Cg-Ltb/Tnf/Lta&lt;tm1Dvk>               Tnf B6.Cg-Trnau1&lt;tm1Dhat> Tg(Col2a1-cre)1Bhr Trnau1&lt;tm1Dhat> B6.129S2-Trnau1&lt;tm1Mmt>                 Trnau1&lt;tm1Mmt> B6.129S5-Tssk1/Tssk2&lt;tm1.1Agr>          Tssk1 B6.129S5-Tssk1/Tssk2&lt;tm1.1Agr>          Tssk2&lt;tm1.1Agr> 129S/SvEv-Oca2&lt;+> Tyr&lt;+>                Tyr&lt;+> 129S1/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+> Mc1r&lt;e> Tyr&lt;+> 129/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;Sl-J>        Tyr&lt;+> 129S1/Sv-Oca2&lt;+> Tyr&lt;+> Kitl&lt;Sl>        Tyr&lt;+> 129S2/SvPas-Oca2&lt;+> Tyr&lt;+> Kitl&lt;+>      Tyr&lt;+> C.D2-Vil                                Vil CPB-WG                                  WG CPB-WV                                   WV Another syntactic outlier; could be processed as a special case: AKR-Chr X/Y&lt;dom>                        Y&lt;dom> Need to investigate: B6C3Fe a/a-Ptch1&lt;mes>                   a-Ptch1&lt;mes> C57BL/6J-mt&lt;FVB/NJ>                     mt&lt;FVB/NJ> This is probably a nonstandard "serial number" n2 from the Sn lab. If serial numbers were more restricted syntactically, they'd be easier to parse out. B10.D2-H2&lt;d>/n2SnJ                      n2SnJ B10.D2-H2&lt;d>/nSnJ-Shh&lt;Hx>               nSnJ-Shh&lt;Hx> B10.D2-H2&lt;d>/oSn-Shh&lt;Hx>                oSn-Shh&lt;Hx> Need to investigate: B6.Cg-pizaa Tg(Isl1-EGFP*)1Slp          pizaa C3H.Cg-T&lt;4Or>/t                         t

Often one has a strain name inside the angle brackets; that appears to indicate something that's not a "phenotypic allele", in which case one wouldn't expect to find it in that report. So these probably do not reflect omissions.