From c0a9159e9320a9ae70189401f2d87547455a180b Mon Sep 17 00:00:00 2001 From: anandhi-iyappan Date: Fri, 8 Nov 2024 13:27:44 +0000 Subject: [PATCH 1/3] the sex description has been modified from genotypic to biological --- src/schema/submission.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/schema/submission.yaml b/src/schema/submission.yaml index 1de5051d..581f90d9 100644 --- a/src/schema/submission.yaml +++ b/src/schema/submission.yaml @@ -1301,7 +1301,7 @@ slots: geographical_region_term: description: >- - The geographical region where the Individual is located. + The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). in_subset: - ontology # range: GeographicalRegionEnum @@ -1315,7 +1315,7 @@ slots: sex: description: >- - The genotypic sex of the Individual (e.g., female). + The biological sex of the Individual (e.g., female). range: IndividualSexEnum biospecimen_age_at_sampling: From cbd923f6f56f975be8ca6a35004cdfca8a1cc67d Mon Sep 17 00:00:00 2001 From: anandhi-iyappan Date: Fri, 8 Nov 2024 13:36:08 +0000 Subject: [PATCH 2/3] updated excel --- spreadsheets/ghga_submission_full.xlsx | Bin 351844 -> 351921 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/spreadsheets/ghga_submission_full.xlsx b/spreadsheets/ghga_submission_full.xlsx index f17e465dbe44627418c02b7a974d3cf9517acc4d..75e80a8289aa7953d71125c6de65b0ab4d48311b 100644 GIT binary patch delta 23765 zcmdU1c|a4_)(=bSR>cLkYKc}6P$U-mN<|GWwJ0DUXxRd3wMbDUidsM**SeIpT4@1^ zh=Lo^mTD?g0|pX(Xem&Pf|mMNBC-jX#1J5aEb~ozjd3{KXq<2G=Rb_UJPH2r7IQ<)1n^+79u7B&KFJGj`~z<+XwKVL z7BYIRpOy2nFAv|IKau%|==#@}zMFjE3#zN{^^nn4vuh!7pzlxjoPrHj#Qf#)iPP@; ztQ+4 z`h?QvLHx}*ZX1rjb$pJso@b&(c4uII!k?c30^fO`AAMi_?eVk5gh%d=N=kIyImO#{ z-8VnK>G&g1 zu_)BS^GWnx#Z%5$za7u2m1WsC-t{;9`5**^>&1kRvN$0EHlfN~Np-k_=m36`LJzpBEu(mdaQl zS_VoOyl6>BhqRpFy1%`(+(=Lr+1ldCrQ|A~NH~h{XGT;2RYrTmj^vc+ybLf%wTn9w$oF)nP=XR!2k455-I%O|PI+m2wtQ07T^m5dV%Xj}3)C z7Ni4-Jh=j*$&`>nAUMndK+zsc6ty4qWHNYp;o`0aK0lQvxno}qmD~W5k4Y(QA~OXb zhCuQVnW!X&(oEpxN>d3+Q#L!&mryO@7gsQ_YwbE2iK`F8}>e?nb*tB6(% zS}pWqM~K#jj;F-uUZ~aP3sC+p$xyp zfF~;v0eAxWuC(wld4`ae2gJ=~kHU!Z<~uC}rBu#?P8D#M*4|3DF_AyBF`?Pj)^JI+ z_u;P!_$#oh6~SK%(`{1VUsK>;o8YgH;IHtnZ28{b>GrZ?GKsPa%*~bLm$c=Nf@&{& zq;h~##$!i|8YAZ{Rmhky4wnC`2>L^3m?#kry0MyY@#bI-zWeZuGq&&`pql~O^4^!Fq z%84mJ47y5K)9vyUm1XVYn(U*$3}Zqmr{AM>U8IKaV7#SaJa%WZv=~H3%1WxrV`CYq zA(L+HS?#K0Opmk33eaC}uKk z3DnYL7In5Qm%^)L)1W5`N=OQa69F86P{{rQMzpMIy4;?V0Y*b2lgk}%%e9BFY0$Wc7B<#fd)LoGxGTh`Igp3I<9*^1&YDmzjtuR7WY?eeIO zf=ZasE*s&5Jg6qJ3Y3H{OyxFZ*iwb0HJnIsSBsHwNpp$J);{;Dyb!X$BKQHCkr~v7ZZwH zg2Q@Kn%^m{kfRVM8oaD4f8#(Xy0S4Ilv_L@8u(%c%bLK%s1C z=NBv!K8*R^-Z;q!ih>&2ZF#&)!fQa8rxe|ZsgUQFUr%N+vIqh1$Y3*#Aq1MQks6>SyEiY*tH18GchI3%y9 zlv0}ITp&%`#&f21oluGzSS;5VTLu&x7N%&g@(fE&B9M05%YR{6E7y$WQUz@1s_6US zv5cw~d-2pOY||BTk#A{!YE+>SB^>M#*IW>FB|l3pA=P!5*UrryjV7=(X? z+m-t`{Eq0W+P6W$sN=4)jb>9IQRikHMLFXpeKf9M+;Pv@)DNn6M?LPmExIXcC&W_l zyP)d&*wezf`l}{wS~X?wt%=U7Mt`hd?i~!|G>SLw+p}X&ogMepCu3LtIyw99lUB1l z3Bi2aO3i!8%CBpbYXbDl4=()tpw*0n7Nfx}$H#U@i-qArd-rJv-udz1f~N=Po;*15 z7sD%A+43)1lv~yBMs9ZU=0G2!7?v&)W_XR&lEVF6Va8VN!P57I86mxcpj%+2eH<}Q z{N?`iv!j1LJLbkGqc6=dT=Zp&r4`oTb1idh7jP?!&gEYrH4>!Zj_YD1(71Y4mET+mH={*Cg6bG0tnd z>(G4Wpq8x+a1iv^+TY4;IauibFwBDhu`}qMy3%EYjIds-?De8y7~CS`Ha%E|U+ae7 za1Xy`3Bb?w8bc1;-E=1QVgKk*3_{Fg*it^kvJ|yJHT=~^`;B5SgB5FVYBTMdldJk5 z=$*dC=nDt!OKVD(rT&Zo)Bp!T_i{NnqFW+eCKD2Fo0*C>u8;b7G9mGHx~XXQ`Y8X& zgp+Ma)zY>XlLwk6M~nL_EsW$LG&Wu}^}SWo-@Ijf_!HAzXYLH!AQ(8Ojvrk}8SzFf zb!B$aY!?zE-soA~lx5OCTu51Bn>_I&44D^jXt0x_6^&w)p z4+YCoIGfbe3wrfS`w1hYXo%V^X+_x+X?8e?m|}FSaZ0W9k8qMriqUtC9<|cHJGmrV z8rYSaI$P*aAbTXDh3BT42nz~iQW5PyZt5H;$KelNMao)DPKYI@pm^rQEGn1+B|-8!imC3#U0;E zBcqCPFS;#E+h`Zyw!qYUQT)6_euP-kc{5`DxlN82_7?Bun_A|LcFh7K{~A|#MRNiT_X$UMa(H2 zw?1WE>ql`8ak+7IN%MvCqiNJF-k$cySFI#Wo)_O3`EFt$?-6T_ndBjJB%N$MIyPn0B zlG5rHo5os1Y$)90SnbhzHg5WfV=28-?uFBMi7!gre=2Y$9+8I|)U(Tshq;V%K;g54p`K0xYc!!g@|E-(3 zK)590>p~~zlr3GA)5;V(k2R6XPnsWbxA?Bq;*hn)D(|G(SA!SR^PLk`|CI1iQ^KmG zgtNamANT4Aa-$yFKN~z~Ih!)7o%G|V)p-+}zj31;rd_EI*|9;gwEROYTiB694msar zHobsdBOm`@qZYP4R+7_b0m@vo1h}49e8S8TXj+SJasA^dY3g>h^-koDoJty+@!geZ z#?#NC8P~d@8J{tC?BNS~%oJw)nXv}rd5M?nLsxvOW%_@GE}g#?rI^YD4EdZi-WjsWYiQ0cWHjgUD`?L7p1qiW9&>~_kGDi~o;^*2GlI#?qi9Ux z(3+_%#*i;iLp~T2Fzfye?$pI-&Sx<=`(kj;LUSfpqB$R@YH&s{3ClJ=0<;}9p4_XN ze$DK&Ld)kiT|+Z4CWTjImCw+e?}ni{({p<<0sTwF1%EW>Xd;^P15M5dChZuS!F`1G z6a5QX3kbMIzI#wZK$WA6W^s=!L38$+p)qHKv+XgoHOxhGCQs4ke2qNe=*F=?GcNg9 z+5XDir3;|Pm1w`b_`L_Pn_2`ZR6@gmf2&h+otk(+e5x?F!pXj8C zeSOWeqdry|+L@Q=;A^=ZyINu-OvOaK308%;+ zobzBY0a^ji^Xl@->s%AGA{2|KT_bD7Mx*Oq4?-<8Yt7~8aC^J;^P_7Q)3x%nT7;lh z{pX5Bu?iKyZ?^_xP^6=x|COzeFelS*@1VceG3<*F)=~hFR80r7vrF75dp37~X#y7K zZpL7U@)+G0Nli>Ze^;p=lo7-PyjV4_*31xK0){cS)CCjJ-4D_PWdtz+$Gy;5?FeE5 zMmXQs#ssMK=(O_v5y1o?-9atRBZvvmt|*7r8omyA#i|baTGBezU_*`x=_ zpDavtsOWe!51_aAjIn&HC))qi}sx%T&j2WYL@n5gw1hnX`rCaV79t9oSGF|#{l z4h<%tdmFTWKT8K|7|M_dR6DBLp!D~IhaD53tD_8)p8(DM<^fy7KrsQ`d)Md!e1tFo zXwKMlXs zbAE|tfYz?KZta+<#bxkrumvi2sN`W3+n@9m+x`1``MuFrJ^zix+I+9Zp!gXE#j;+C zY6&$LgJ4vSTJ%p?4^;nWfb659X9FKw*TL0ZqFfzxJMjJ^mf0cOLn-LP6E8;fU(tWW z>Nt%MCPUkQe0@y*wf)Bt!esdSk1xjrX#Qu>iydW{`t+dtzm#+xgMa$Le1kaK3achL#>+;h=c!vObb0UmLo=FE6A zrySK`#F?*l7@01hC8p$cXLkOl5P4ne3z;<=GVVAW9;@Xv(( zKIwqQV$bj{>UcD2BvX*?_^az8q+^2g8leMdCmg34a3(!Z%T;e_)dvj zICvCl2ajS~j3~`ekE%UEl|sje(iR#K8Nk`ka&MY%=F_4y&4f~Z<+J-IoHW-L>2-`T za}9zBJ(81l%7A!?E80WAKvT~F=o(Aa;Dwnnwk04QVm5Rh0o1;P9O!&Y1Af*R1wx3=N>z5IL(*cRvPEVuZ!e)J#XO};YZ*M8 zZ*M|Vinw5Wmn)}JLI6r>0i=|132aDU&xV?)MEOJLd2OscR9iz$mGTIni^~CZ5@?j> zt9lOyUVgZ0B`)jp)ZmrKTYAfRDQT(;X7~}ksn?LJ@9p%dtBlC-n|t+)OKH9iINZL& z2K3Z?{Ta*!QTp2*4B(%b@%j2`uE^E0DF#Vo|C z;iB$eAMG)`=7;?H!+pbFERm~~O2dsV$W?+fewQ9{HOd8_X`s5I=WfI|AVX>Hc#=MH z)vyV_ru#O_kMUpYsU)W}J@L!Ns9rgYyqcLV^TfYTP<>T@LGcv$jm^D(2lPtlZeI9z zkelAQY!$bCB@XBPwgGNN?;Y^xfiEY}fAGSa%~4V6f0wbL)=gK|(I-XePgT9$*vQRE zPv6*}?}gEHJ#YLh{j;ga4RjlC{3L`{jOAAjJJN8tnN!DT(VG6a`_>5fR%Bw|!2}Gl zkLc0Q-8VF*bKqe_WE0njd&^hha77k385BU}qo$0#_ROF}9O?>f_=Bl2R zo_xGE85V8(QUlyf4Q>ATYtOv_@V$sA5xy{q{jEL2lvV>x4XUKQsk)`b#;}{qJsU$j zz0()}Ccd2iux_6?}UG(TG8{r8snn>pNqMy zG2;UDD6G#i+P!llf8PP(nxdLAEcmRki*{|eCl!`8|3crCcGA!1%+;bvJ3swKu>SiA z$DN@Kd!2uNkji=g>j}9AtCJ2-KDe645)-QI5)CGJ<(Egf><)Dj+%|8u{jxkvk^C^w zjo$=MTp74M%WwmpqgcbxQ`3QKl>3DlAH9deT`<9=*6Uflr;lhPb+Td1GJ;YyHeVjz zv}Y3zSGU1{{l{^=k0YQ}c#y@d3il`vG=5Gge7J^UcX#duJ?kBIkqxA@0HCkUiNKJYa=|vCGjVk!Cr=o5ABqD)DpvBA6YAz&x6AV5SPc}%9^9g zX(XAPmXnz&Rq&b8DgqVwOY7@GI1I78r7B2LlPRWo^0;t~lm>vbS}IPnAPKf+7T>xTdAqA9P6}8(9hULs=39V)~04@5wD;MO|7NED^PGm;n4L z2PB0kiQQTMB)Te%=$Rc9BvgpP5DswX3;w@zrD=l3crxcXCp$x47ShtNhzOEFfVdUV zWg(Ihc~w{EX&Mz`GQ@4OE%~66UF9q7>L>{1a-v{~B!iQl)mkuL90%74TAZ!L{1*gE z(o-Is4@;A2tvOODl+{@RN*1L7x+J$b6K-!M*NB9)=EkJ=nex_-5HcJjOd^7|8fgs` zeo@`ZjV|?uI4`0pG$3oM<0y>7sJ{7EO1*8m^1N*n^!yqsJwF2ZDnY)=>G@^I*Hq-I z6!{9%^M%OQ&{FTL&OC2=hvZZWvuz@QD60c2I-eCpHx>{SNp2>dylhzrlnum5(PAR` zF6UW696dvibUX+YWF3;Wjjbm^*_?8UxPdFrEiO;-WOj0C{8r13wtF;=f?i2d$aX>q z(jqQ5jsrS6NN}5|j!WPp#vtUjNEcNk6v2uFPez1?DO2$UlyykbQU&~po{jBY4&-uL zyj+I2eX8*Bb%G@kIoS+xi%{0gev)mB#0n#O--#N8(-#v-M~-vk+5rGP5Oq5xl3M=5C-wR4;1bCTEhM ztgOuR%%n^pP2n!$D*|9VOrUu(Iy+a&XsMZ!;*@>qAJA-}6N{*vO!yidh^rOHZ8?<< z<;;$1#F7d89A<~0RTM2Pt;pm*NJFfqRi0c00wrDbVSFfC@=r0u_sn5*RF^`b_|vn7tE$Zdg` z(loGN2rDEdVu+i?5SO%+_ydK4D^8&@13Cn>Jw=(s9C<5kPrm$8CXrJvhg{dz6)$1P zTjg@^=VCsODQuhi;BI=5xMs3cPU6anGgGLF>X33V6aWhj=JNsEdjII~uvikaUD80{ z14VmMP3bh-HISW5Chbg0Bi3XE3R`V&m&V;mgY9hXNsKl3hBw&Ok-Z;`flG6TFM_K% zVbYKGK=3(!37-n_z*r7AD&IoYF^V?}_hY|*g-k~Eyi`Ag0%DIi}>gTPnRCh(-9juJDK)AUzY z@`F9dha&mGG~`2){J<0DrKar3F(Gm3WTwcM$PsXIveRK!Tkh_ILbG_1|Xavf;FSEktCfPYFYNU;u5R6<={MicI4OpR0cEwzN_N0vK5Wf)<#bt5{DrA; zt@YldAg(wK7KTvx!le=iZzNomAn_B5H(^uv`^wHoG^Z>{muHqWkwASWpLFmhJ0(^6 z0%Fw5{NvIUpL=_9x0Hg6`>`P7F-Rq|4@qm{eqv-W_GUc`covY?cA{o#!SK`MDO6b0 zxe;f{9Qh1C>|WcEn&29vg2|`-rw|w0?xV}AYAAa24rd&7I&O;P;%SRL_hnTF6to4` zj4deVe9knwmphzIdcinsXt465BeTCgV)5}2GnWzW-Z$md;uT(crbj;7uzai^xc`yk zefwwDp~Z2jw)A*&ociW{k{KsL!p`C^8h)`3zvdx+#b@|A!Oi9taK7}#$y>N_%ME|J zI3i<X}!S&R;ksTqWkth<`f=k~eTm%|~ zjf9u16E(T*7G7%7ScE5wA1x(b^&k1&Ck7iI8hCtW;Cy4u-3NbSEpC&-;wMY-8dugB z6ZUv19$>Bx-6H6X4ZQmY2R{90o>>n#FR|(WVoS;fOr0cSDN4BrQ0jZ*R_%5wLNBv< zl7D79uQQnbJ^hM@!?d z>}T*6L2vKf7G!uB>!PBxU$nDEFxigFPg^hIhu#v<0(ImfHWB z8{YZLOk0bSr4E1UN8~(Q8b^Jr(7hxfKgwu-Frg{th(^rq?;=RO+uyD4y7NENo)mf? z5NwU1Z#E&87d9La1jo?9HWOk+q4z=NCI1{ONr+nxHO5e}Y?9-I;pxl-jNmD=$BI5@ zRYuj@{>?42g>$e>g@UEu6eN3~@&sDaZ9$uDh!aX1@`S-{^ldi8iKX88!b@%RZ)}K@ z;k*Wr&nKJ~N7Trl2auNX2w~!~8hK{`iNqtE5s$6qv>Qr>SIw^_zL+iu|6+uF!UFrG zQAP1TJDzsAQ&32HCag6+J|@zBXXM(6k*i&!rrg{`W`TQl#SSBlP0v0ujj=L~xMj6u zTg5ah_%Jz&JvNhy4-gkynnhmRV1LE0=%Qm$QSG;0LG3dA z0~Gs91_@4+5}e=ja@sV@&b-R`Iq}83c17%_~1LNX2wjy z%)se|V^{N5308$u!fhfzZA`o+!MMd?b*#N$Q+Ppm7OOUWCf_*lv%=8Tv5s9%#az3H ztn;-MGx@Uu7Z(<`D~l3#Zf>|90!P`*pkZ8m7P5A|xKIm}sXS`M@iGVigCPsR>wq zbJq%ILiz$U=P5C0&aGrL=cFIeoRc@GX$Byk%qk9^t;Sge$tEMTX6|5UW($UVsp|4g zEneu;aVB$<8fO*blVA>-b0r4nP7Kb$XwDaM)j2CMvDl8*jNPps&45>tYc4y;6)j++ zxte?kCNnk@(l4VqPkD^yyvGO4+53(fCIE?r?Lc$hX@%x&KM~FO1_oyjH0KNRdNc!GWn;uq&a0_L zrI~^fv}Triqvb1{uO=VmrcLFY(rNpon&RZn9e>-s*H)lR?qPRa9{ZZ9XAc|Rw)Mpc zYTEftup@NkT(*X4%QPq|36^3JgfIwh0~i!3Zsy;lt6k#t?G>0;gCqt9TDebc(PpC~c$Vvu5p<{xw?3xtlR~S-1^4=Wo4y($Sg$ zx82{Qnm#n68%%(Dp}N`PwQ7b$GeBAMYJxH(oV$x{fCb7BVgl4#0FUjiu7$3UXLak^4Ggt+vbbHz*cGt}x>zveE zslW^jiWMk|Ggu861U)ebO1=qQ2{h`71Ll}lgVczFlNdm+23x1#yBFNr9rt;CU#J3A zYp+wzs=B?uWen&`Kt#U5#001hJq9-vU|<4Xj#~zo^BXY%TI5V+%G4Dmpx2B~`yix! zcm`1zpbQ}zRD!FA{`0fQ6PUq$u4`~>tKp8pL! z7*G!4`&C=I=LvRH*#`ZJG7&-=M)zKc(QF4`^x7Z-qkSi1QLMtCNXMWUib0UNTeF-< zKkcQu7@)h>TB{(`d;X|pC}?)M(~@d}Zms);YWMt6OU|nM1n-u(K<^swB`8CPN$>fi z4nsk|G3lN^>X7pQF;SmCVuXT0#-#WB5!FMW6T=(p7*te37ZaG6fc}QRcj5dNOn`ca zggGNaIkFBh0k3Ym4teXZ?EIU-y96&CU;;Fz$=cR2R$5{LUfo{Rnln}b)o;xJ<=t0} z+A`TCc2AWz88zCjtHx-y?J%0{X*A7ryJTD7EsXBHaXio*2+Ux4V^EC6qIeU7VlpcG zBe#dJE~dxR{%7ZpSk=VT;yVmcq)wCd;Ljg5Cr-+N(`!urujY?~fXUx8e|(Jzc>R#g zYfy%8Cj8Fx$9Kd8pu^u=vb8qJ`t9Kvs6A7KYQP5_6VUTC7mD+{++-X8CIET*q#w20 zpkV^ko?h!$1Flm{K+kh?{o<@^OpJ*Pzm^ojDon<~tXI z;4Xw9(7c^5#Gq)2L6LqNmHkz>QPCHJJYVzXl==71AF)a`)jhjd^wSf%uMu@Qf5e&s z_Jzs+=KOK!Fd6LmV_%s3|I8l;2NN*JLx;W+7kK&Hb6<`!NOO9ieBxTCt^dGc7tnHU ziDeD1tJ>E^ZC@!9ynenJ9bAV16QF#u8qHbPm~0EoLGA`OXf*mWSRnwT*`9`)mLu(Z z7AoC-TUUrN4@klw7>h+PM@3M*|EtTxpqPTn{@u5S&{w0yvm8S>f5Zv}2Y~W=UxGvB1 za{kWOI`Eb|Mfud!(O%L~Q{Ah)p_?q=L z1u_fraP%)aUH3B`sXWBwjUIyh{-qyPx{hSQDAEB|m5!wlI1P^ zOkbK(6<56+1Pr8m(XlK_3sTOXwMYTo)m3d@)m7ic)!*EIlmKOQ)vF&I>UI#ITjIV< z2*dHatE+zWzbFd=Z*R}FkY!-05un@iINeoOeaiygI4VG?s{fiAKzVkfGY)#dM#Ii?j&lmYm=l+(sb!6Fsxz6DHovV&X326^$ z{4cD-*5r;$+_^b%!EWcMwGOmP5cjyBS@a1r$Fg4>cUC4^#jq5dha6d52%iHl$&pGj zA-Fk?Bdrm`A}$%o%3xXD1h_*^RCLu_!V(%Vku)O9)kFdb?rh+^Cr_fvke6@5vKj!( z8wkj|MTw9Z+@3Z;(F8i%3gY0l7ipz3KJt3b28bk(!uo12*G;_^=eO)b<$H8P%um?) zB;arpjo1&5>rG5u_3TiB@=d#GdB^pPZmW*C*28GaRYzp{u+w&`qi4Cp63D8fZ^!CK zxvNO|Jssb?c^MA3Vk-OI4gE=JtM}^fT&CJ{`-XmLH-!*^{+{lm&iMv&y8k-M&)~L) zY9H?pgP+Y+N8c+9)~{6^RXgJM>Zy)4ti|8bS01rPIN|G6O9Cgn?J(8R{Ehe(-P-~; z;lEWKu?<}COJBc7nZ3#dzfg60unT^&-UD`w3;xqjlsfqInnn0Gh~TbM^>H5~?_hrU z?{F}|kbTn?Zxlf?#Iq$X_))6uy{&4I)L5a_cPBxs}Md`aZ|?*lmvZaqLl>@uOACpKL~!k6I5?En6+L2-v-A zorB)6ar&>`AnmF*?h(_?4u?B%O!JyLg1XORpLfrf|{WA(cwn(5ZF_ciwVxQQ?IhkPCmE~2US8nJzly(;N}8^X@*M)$JSJS^#H zo{+EgavZK`u_n2>f*x{`m*hThNAw#zpS{l=Kc2nJy+^-?Ze7m|_Q2t;)f;FC^!tA0 zRuh#d(aLj={n35ygO}$nxoiecU5mqsn>4x4S9EVR^60r1GY{liLLBi*bxa~?fWY31 z{B>B@8us_fT}s1EMh>h~*5h$hU$0&JEiIJ)Yn Date: Fri, 8 Nov 2024 13:45:14 +0000 Subject: [PATCH 3/3] updated build documentation --- .../Individual_geographical_region_term.md | 2 +- docs/schema_markdown/Individual_sex.md | 2 +- docs/schema_markdown/Ontology.md | 2 +- .../geographical_region_term.md | 2 +- docs/schema_markdown/index.md | 4 +- docs/schema_markdown/individual.md | 74 ++++++++++++++++--- docs/schema_markdown/sex.md | 2 +- 7 files changed, 71 insertions(+), 17 deletions(-) diff --git a/docs/schema_markdown/Individual_geographical_region_term.md b/docs/schema_markdown/Individual_geographical_region_term.md index 1b1dc7ab..b0e6fa80 100644 --- a/docs/schema_markdown/Individual_geographical_region_term.md +++ b/docs/schema_markdown/Individual_geographical_region_term.md @@ -2,7 +2,7 @@ # Slot: geographical_region_term -The geographical region where the Individual is located. +The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). URI: [GHGA:Individual_geographical_region_term](https://w3id.org/GHGA/Individual_geographical_region_term) diff --git a/docs/schema_markdown/Individual_sex.md b/docs/schema_markdown/Individual_sex.md index 4df2a371..5f1d8bec 100644 --- a/docs/schema_markdown/Individual_sex.md +++ b/docs/schema_markdown/Individual_sex.md @@ -2,7 +2,7 @@ # Slot: sex -The genotypic sex of the Individual (e.g., female). +The biological sex of the Individual (e.g., female). URI: [GHGA:Individual_sex](https://w3id.org/GHGA/Individual_sex) diff --git a/docs/schema_markdown/Ontology.md b/docs/schema_markdown/Ontology.md index c0eade5c..c42afa52 100644 --- a/docs/schema_markdown/Ontology.md +++ b/docs/schema_markdown/Ontology.md @@ -32,7 +32,7 @@ URI: [GHGA:ontology](https://w3id.org/GHGA/ontology) * [diagnosis_ids](diagnosis_ids.md) - One or more diagnoses that the entity is associated with at the time of retrieval from the organism. The diagnosis is captured using a code from ICD-10 (WHO version). Please restrict the ICD code to the chapter letter and two digits for the main diagnosis (e.g., E10, C01). * [diagnosis_terms](diagnosis_terms.md) - The ICD-10 terms corresponding to the ICD-10 codes (e.g., Type 1 diabetes mellitus, Malignant neoplasm of base of tongue). * [geographical_region_id](geographical_region_id.md) - The geographical region where the Individual is located. - * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. + * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). * [phenotypic_features_ids](phenotypic_features_ids.md) - The corresponding ID to the HPO vocabulary (e.g., HP:0002732, HP:0012735, HP:0002615). * [phenotypic_features_terms](phenotypic_features_terms.md) - The phenotypic feature concepts that the entity is associated with at the time of retrieval from the organism. The Phenotypic Feature is captured using a concept from the Human Phenotype Ontology (e.g., Lymph node hypoplasia, Cough, Hypotension). diff --git a/docs/schema_markdown/geographical_region_term.md b/docs/schema_markdown/geographical_region_term.md index ba2e3590..bcbb1e01 100644 --- a/docs/schema_markdown/geographical_region_term.md +++ b/docs/schema_markdown/geographical_region_term.md @@ -2,7 +2,7 @@ # Slot: geographical_region_term -The geographical region where the Individual is located. +The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). URI: [GHGA:geographical_region_term](https://w3id.org/GHGA/geographical_region_term) diff --git a/docs/schema_markdown/index.md b/docs/schema_markdown/index.md index 4918ad33..0b197e8b 100644 --- a/docs/schema_markdown/index.md +++ b/docs/schema_markdown/index.md @@ -164,7 +164,7 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi * [ResearchDataFile➞format](ResearchDataFile_format.md) - The file format of the Research Data File (e.g., FASTQ, uBAM, FASTA). * [geographical_region_id](geographical_region_id.md) - The geographical region where the Individual is located. * [Individual➞geographical_region_id](Individual_geographical_region_id.md) - * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. + * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). * [Individual➞geographical_region_term](Individual_geographical_region_term.md) * [included_in_submission](included_in_submission.md) - Whether a File is included in the Submission or not. * [File➞included_in_submission](File_included_in_submission.md) @@ -238,7 +238,7 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi * [ExperimentMethod➞sequencing_layout](ExperimentMethod_sequencing_layout.md) * [sequencing_read_length](sequencing_read_length.md) - Length of sequencing reads (e.g., long or short or actual number of the read length). * [ExperimentMethod➞sequencing_read_length](ExperimentMethod_sequencing_read_length.md) - * [sex](sex.md) - The genotypic sex of the Individual (e.g., female). + * [sex](sex.md) - The biological sex of the Individual (e.g., female). * [Individual➞sex](Individual_sex.md) * [software_versions](software_versions.md) - key/value pairs where key corresponds to a software name and value corresponds to a version descriptor (e.g., `salmon` = '1.3.0', `trim-galore` = '0.6.6', `bedtools` = '2.29.2'). * [AnalysisMethod➞software_versions](AnalysisMethod_software_versions.md) diff --git a/docs/schema_markdown/individual.md b/docs/schema_markdown/individual.md index 942ff22d..eb9a1101 100644 --- a/docs/schema_markdown/individual.md +++ b/docs/schema_markdown/individual.md @@ -1,23 +1,77 @@ -# Slot: individual +# Class: Individual -The Individual associated with an entity. +An Individual is a Person who is participating in a Study. -URI: [GHGA:individual](https://w3id.org/GHGA/individual) +URI: [GHGA:Individual](https://w3id.org/GHGA/Individual) -## Domain and Range +[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[IndividualSupportingFile],[IndividualSupportingFile]-%20individual%201..1>[Individual|phenotypic_features_terms:string%20*;phenotypic_features_ids:string%20*;diagnosis_ids:string%20*;diagnosis_terms:string%20*;sex:IndividualSexEnum;geographical_region_term:string%20%3F;geographical_region_id:string%20%3F;ancestry_terms:string%20*;ancestry_ids:string%20*;alias:string],[Sample]-%20individual%201..1>[Individual],[Submission]++-%20individuals%201..*>[Individual],[Sample]-%20individual(i)%200..1>[Individual],[IndividualSupportingFile]-%20individual(i)%200..1>[Individual],[Submission]-%20individuals(i)%200..*>[Individual],[Individual]uses%20-.->[IdentifiedByAliasMixin],[IdentifiedByAliasMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[IndividualSupportingFile],[IndividualSupportingFile]-%20individual%201..1>[Individual|phenotypic_features_terms:string%20*;phenotypic_features_ids:string%20*;diagnosis_ids:string%20*;diagnosis_terms:string%20*;sex:IndividualSexEnum;geographical_region_term:string%20%3F;geographical_region_id:string%20%3F;ancestry_terms:string%20*;ancestry_ids:string%20*;alias:string],[Sample]-%20individual%201..1>[Individual],[Submission]++-%20individuals%201..*>[Individual],[Sample]-%20individual(i)%200..1>[Individual],[IndividualSupportingFile]-%20individual(i)%200..1>[Individual],[Submission]-%20individuals(i)%200..*>[Individual],[Individual]uses%20-.->[IdentifiedByAliasMixin],[IdentifiedByAliasMixin]) -None → 0..1 [Individual](Individual.md) +## Uses Mixin -## Parents + * mixin: [IdentifiedByAliasMixin](IdentifiedByAliasMixin.md) +## Referenced by Class -## Children + * **[IndividualSupportingFile](IndividualSupportingFile.md)** *[IndividualSupportingFile➞individual](IndividualSupportingFile_individual.md)* 1..1 **[Individual](Individual.md)** + * **[Sample](Sample.md)** *[Sample➞individual](Sample_individual.md)* 1..1 **[Individual](Individual.md)** + * **[Submission](Submission.md)** *[Submission➞individuals](Submission_individuals.md)* 1..\* **[Individual](Individual.md)** + * **None** *[individual](individual.md)* 0..1 **[Individual](Individual.md)** + * **None** *[individuals](individuals.md)* 0..\* **[Individual](Individual.md)** - * [IndividualSupportingFile➞individual](IndividualSupportingFile_individual.md) - * [Sample➞individual](Sample_individual.md) +## Attributes -## Used by + +### Own + + * [Individual➞phenotypic_features_terms](Individual_phenotypic_features_terms.md) 0..\* + * Description: The phenotypic feature concepts that the entity is associated with at the time of retrieval from the organism. The Phenotypic Feature is captured using a concept from the Human Phenotype Ontology (e.g., Lymph node hypoplasia, Cough, Hypotension). + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞phenotypic_features_ids](Individual_phenotypic_features_ids.md) 0..\* + * Description: The corresponding ID to the HPO vocabulary (e.g., HP:0002732, HP:0012735, HP:0002615). + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞diagnosis_ids](Individual_diagnosis_ids.md) 0..\* + * Description: One or more diagnoses that the entity is associated with at the time of retrieval from the organism. The diagnosis is captured using a code from ICD-10 (WHO version). Please restrict the ICD code to the chapter letter and two digits for the main diagnosis (e.g., E10, C01). + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞diagnosis_terms](Individual_diagnosis_terms.md) 0..\* + * Description: The ICD-10 terms corresponding to the ICD-10 codes (e.g., Type 1 diabetes mellitus, Malignant neoplasm of base of tongue). + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞sex](Individual_sex.md) 1..1 + * Description: The biological sex of the Individual (e.g., female). + * Range: [IndividualSexEnum](IndividualSexEnum.md) + * [Individual➞geographical_region_term](Individual_geographical_region_term.md) 0..1 + * Description: The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy). + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞geographical_region_id](Individual_geographical_region_id.md) 0..1 + * Description: The geographical region where the Individual is located. + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞ancestry_terms](Individual_ancestry_terms.md) 0..\* + * Description: A person's descent or lineage from a population. + * Range: [String](types/String.md) + * in subsets: (ontology) + * [Individual➞ancestry_ids](Individual_ancestry_ids.md) 0..\* + * Description: A person's descent or lineage from a population. + * Range: [String](types/String.md) + * in subsets: (ontology) + +### Mixed in from IdentifiedByAliasMixin: + + * [IdentifiedByAliasMixin➞alias](IdentifiedByAliasMixin_alias.md) 1..1 + * Description: The alias for an entity at the time of submission. + * Range: [String](types/String.md) + +## Other properties + +| | | | +| --- | --- | --- | +| **Aliases:** | | subject | +| | | patient | diff --git a/docs/schema_markdown/sex.md b/docs/schema_markdown/sex.md index 5f178a05..4c318e07 100644 --- a/docs/schema_markdown/sex.md +++ b/docs/schema_markdown/sex.md @@ -2,7 +2,7 @@ # Slot: sex -The genotypic sex of the Individual (e.g., female). +The biological sex of the Individual (e.g., female). URI: [GHGA:sex](https://w3id.org/GHGA/sex)