Release Notes

PMN Release 12.5

Released: 
April 2018
Release Information: 

The data content of all 77 databases are described on our Content Statistics page while the data sources and methods for each database's contruction are listed on the Databases Overview page

Past releases are described in the Release Notes Archives and Databases Overview Archives

Parent

Overview
Update Of: 
PMN Release 12.0
Overall Highlights: 

We are pleased to announce PMN12.5 release. In this release we added locus IDs to genes in all PMN databases. The locus IDs were extracted from public genome releases that were used in constructing the PMN metabolic pathway databases. Protein sequence IDs from the genome releases are associated with proteins. The locus IDs, along with protein sequence IDs, should greatly facilitate data query and usage. Additional data cleaning was done to several databases, most noticeably in AraCyc where we removed more than 140 redundant gene entries.

PMN Release 12.5
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 12.5 1200 136293 6498 5497 10836
AhalleriCyc 1.5 490 4741 3232 2371 3716
AhypochondriacusCyc 1.5 483 4608 2945 2242 3869
AlyrataCyc 1.5 502 5503 3211 2382 3834
AmborellaCyc 1.5 490 4585 3128 2396 3890
AraCyc 15.5 610 5447 3556 2967 6117
BananaCyc 1.5 480 6588 2988 2293 3874
BarleyCyc 5.5 487 4659 2942 2337 4024
Boleracea_capitataCyc 1.5 483 6477 3100 2321 3765
Boleracea_oleraceaCyc 1.5 500 10525 3320 2461 3815
BrachypodiumCyc 5.5 495 5338 3033 2320 3839
Brapa_fpscCyc 1.5 500 7646 3211 2409 3836
BreadwheatCyc 1.5 540 22445 3470 2774 4379
BstrictaCyc 1.5 493 5080 3171 2349 3750
Carietinum_icc4958Cyc 1.5 520 5662 3349 2485 4050
CarrotCyc 1.5 496 6283 3062 2343 3882
CassavaCyc 7.5 513 6296 3178 2422 4037
CastorbeanCyc 1.5 534 6141 3761 2917 4215
CgrandifloraCyc 1.5 489 4749 3121 2308 3697
ChineseCabbageCyc 5.5 497 7868 3206 2373 3786
ChlamyCyc 7.5 379 2772 2471 1799 3666
ClementineCyc 1.5 509 5191 3140 2377 4008
CocoaCyc 1.5 509 5181 3192 2442 3982
CommonbeanCyc 1.5 515 5582 3144 2412 3997
CornCyc 8.5 556 7372 3259 2614 4718
CroseusCyc 1.5 543 15565 3431 2696 4289
CrubellaCyc 1.5 486 5032 3141 2327 3687
Csativa_pkCyc 1.5 502 5047 3138 2382 3905
CsubellipsoideaCyc 1.5 304 2053 2195 1638 2872
CucumberCyc 1.5 495 4382 2999 2331 4045
EgrandisCyc 1.5 519 7909 3185 2431 4031
EsalsugineumCyc 1.5 490 4958 3141 2322 3711
FlaxCyc 1.5 526 9106 3322 2576 4062
Fvesca_vescaCyc 1.5 499 5125 3069 2341 3878
GraimondiiCyc 1.5 506 7371 3185 2410 3966
GrapeCyc 7.5 511 5790 3191 2463 4006
KlaxifloraCyc 1.5 463 10324 3027 2311 3743
LjaponicusCyc 1.5 512 6967 3236 2497 4010
LperrieriCyc 1.5 486 5028 2932 2257 3757
McommodaCyc 1.5 308 1812 1976 1447 2763
MdomesticaCyc 1.5 521 13070 3311 2597 4123
MguttatusCyc 1.5 492 5517 3121 2393 3820
MossCyc 6.5 404 4937 2821 2072 3224
MpusillaCyc 1.5 307 1774 1943 1464 2822
MtruncatulaCyc 1.5 541 7868 3334 2541 4110
Ntabacum_tn90Cyc 1.5 513 9084 3175 2570 4385
ObrachyanthaCyc 1.5 491 5295 2992 2310 3816
OglaberrimaCyc 1.5 487 5531 2987 2301 3787
OilseedrapeCyc 1.5 513 17724 3385 2573 4151
OlucimarinusCyc 1.5 284 1538 1790 1349 2689
OpunctataCyc 1.5 487 5246 2981 2299 3804
OrufipogonCyc 1.5 489 5509 3048 2346 3824
OryzaCyc 5.5 547 6311 3278 2625 4525
OthomaeumCyc 1.5 437 4604 2761 2120 3644
PapayaCyc 6.5 488 4339 3121 2354 3750
PineappleCyc 1.5 469 4761 2911 2207 3759
PoplarCyc 10.5 538 7988 3282 2498 4106
PotatoCyc 4.5 524 6390 3203 2625 4381
PpersicaCyc 1.5 512 5401 3136 2396 3970
RedcloverCyc 1.5 520 7515 3287 2525 3974
RedsageCyc 1.5 498 5046 3074 2355 3828
SelaginellaCyc 6.5 419 4819 2761 2103 3345
SetariaCyc 5.5 491 6289 3003 2290 3818
SoleraceaCyc 1.5 498 4146 3039 2409 4250
SorghumBicolorCyc 5.5 478 5961 2961 2294 3812
SoyCyc 8.5 601 10613 3496 2760 4797
SpirodelaCyc 3.5 450 3635 2719 2066 3596
SugarbeetCyc 1.5 507 4563 3127 2365 3944
SviridisCyc 1.5 494 6137 3013 2273 3814
SweetorangeCyc 1.5 516 5202 3154 2410 4045
SwitchgrassCyc 5.5 526 13998 3342 2580 3995
TomatoCyc 3.5 535 6267 3279 2677 4388
TparvulaCyc 1.5 490 4965 3162 2347 3727
VcarteriCyc 1.5 312 2189 2125 1559 2808
WheatACyc 3.5 502 6307 3114 2422 3889
WheatDCyc 3.5 492 6540 3072 2362 3790
ZmarinaCyc 1.5 431 3816 2635 1951 3435

PMN Release 12.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 12.0 1200 136453 6499 5503 10836
AhalleriCyc 1.0 490 4743 3232 2371 3716
AhypochondriacusCyc 1.0 483 4609 2945 2244 3869
AlyrataCyc 1.0 502 5504 3211 2384 3834
AmborellaCyc 1.0 490 4586 3128 2397 3890
AraCyc 15.0 610 5716 3557 2971 6117
BananaCyc 1.0 480 6589 2988 2298 3874
BarleyCyc 5.0 487 4660 2942 2339 4024
Boleracea_capitataCyc 1.0 483 6478 3100 2322 3765
Boleracea_oleraceaCyc 1.0 500 10526 3320 2462 3815
BrachypodiumCyc 5.0 495 5339 3033 2324 3839
Brapa_fpscCyc 1.0 500 7647 3211 2411 3836
BreadwheatCyc 1.0 540 22446 3470 2778 4379
BstrictaCyc 1.0 493 5081 3171 2350 3750
Carietinum_icc4958Cyc 1.0 520 5664 3349 2489 4050
CarrotCyc 1.0 496 6284 3062 2345 3882
CassavaCyc 7.0 513 6297 3178 2424 4037
CastorbeanCyc 1.0 534 6142 3761 2922 4215
CgrandifloraCyc 1.0 489 4750 3121 2309 3697
ChineseCabbageCyc 5.0 497 7869 3206 2375 3786
ChlamyCyc 7.0 379 2888 2471 1803 3666
ClementineCyc 1.0 509 5192 3140 2379 4008
CocoaCyc 1.0 509 5182 3192 2446 3982
CommonbeanCyc 1.0 515 5583 3144 2416 3997
CornCyc 8.0 556 7507 3259 2616 4718
CroseusCyc 1.0 543 15566 3431 2700 4289
CrubellaCyc 1.0 486 5033 3141 2328 3687
Csativa_pkCyc 1.0 502 5048 3138 2386 3905
CsubellipsoideaCyc 1.0 304 2054 2195 1640 2872
CucumberCyc 1.0 495 4383 2999 2333 4045
EgrandisCyc 1.0 519 7910 3185 2434 4031
EsalsugineumCyc 1.0 490 4959 3141 2323 3711
FlaxCyc 1.0 526 9107 3322 2579 4062
Fvesca_vescaCyc 1.0 499 5126 3069 2344 3878
GraimondiiCyc 1.0 506 7372 3185 2412 3966
GrapeCyc 7.0 511 5791 3191 2466 4006
KlaxifloraCyc 1.0 463 10325 3027 2313 3743
LjaponicusCyc 1.0 512 6968 3236 2501 4010
LperrieriCyc 1.0 486 5029 2932 2259 3757
McommodaCyc 1.0 308 1813 1976 1448 2763
MdomesticaCyc 1.0 521 13071 3311 2602 4123
MguttatusCyc 1.0 492 5518 3121 2396 3820
MossCyc 6.0 404 4938 2821 2074 3224
MpusillaCyc 1.0 307 1759 1943 1464 2822
MtruncatulaCyc 1.0 541 7869 3334 2546 4110
Ntabacum_tn90Cyc 1.0 513 9085 3175 2574 4385
ObrachyanthaCyc 1.0 491 5296 2992 2312 3816
OglaberrimaCyc 1.0 487 5532 2987 2304 3787
OilseedrapeCyc 1.0 513 17725 3385 2575 4151
OlucimarinusCyc 1.0 284 1539 1790 1352 2689
OpunctataCyc 1.0 487 5247 2981 2302 3804
OrufipogonCyc 1.0 489 5510 3048 2349 3824
OryzaCyc 5.0 547 6414 3278 2629 4525
OthomaeumCyc 1.0 437 4605 2761 2123 3644
PapayaCyc 6.0 488 4340 3121 2358 3750
PineappleCyc 1.0 469 4762 2911 2209 3759
PoplarCyc 10.0 538 7989 3282 2502 4106
PotatoCyc 4.0 524 6391 3203 2629 4381
PpersicaCyc 1.0 512 5402 3136 2400 3970
RedcloverCyc 1.0 520 7516 3287 2529 3974
RedsageCyc 1.0 498 5047 3074 2358 3828
SelaginellaCyc 6.0 419 4820 2761 2105 3345
SetariaCyc 5.0 491 6290 3003 2293 3818
SoleraceaCyc 1.0 498 4147 3039 2412 4250
SorghumBicolorCyc 5.0 478 5961 2961 2294 3812
SoyCyc 8.0 601 10819 3496 2764 4797
SpirodelaCyc 3.0 450 3636 2719 2069 3596
SugarbeetCyc 1.0 507 4548 3127 2364 3944
SviridisCyc 1.0 494 6138 3013 2276 3814
SweetorangeCyc 1.0 516 5203 3154 2412 4045
SwitchgrassCyc 5.0 526 13999 3342 2583 3995
TomatoCyc 3.0 535 6268 3279 2682 4388
TparvulaCyc 1.0 490 4966 3162 2348 3727
VcarteriCyc 1.0 312 2190 2125 1561 2808
WheatACyc 3.0 502 6308 3114 2425 3889
WheatDCyc 3.0 492 6541 3072 2365 3790
ZmarinaCyc 1.0 431 3817 2635 1952 3435

PMN Release 11.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 11.0 1213 140581 6051 5128 11114
AraCyc 14.0 619 5472 3482 2802 5485
BarleyCyc 4.0 540 4662 3033 2942 3637
BrachypodiumCyc 4.0 531 5319 3004 2285 3567
CassavaCyc 6.0 567 6371 3183 2386 3808
ChineseCabbageCyc 4.0 533 7825 3146 2331 3522
ChlamyCyc 6.0 373 2768 2435 1750 3221
CornCyc 7.0 545 6778 3151 2525 4256
GrapeCyc 6.0 557 5799 3182 2421 3784
MossCyc 5.0 473 4952 2801 2035 3135
OryzaCyc 4.0 543 6198 3223 2487 3906
PapayaCyc 5.0 538 4345 3111 2329 3552
PoplarCyc 9.0 599 7996 3305 2509 3936
PotatoCyc 3.0 558 5790 3122 2413 3706
SelaginellaCyc 5.0 481 4840 2811 2105 3261
SetariaCyc 4.0 549 6045 3028 2284 3635
SorghumBicolorCyc 4.0 540 5939 3017 2276 3676
SoyCyc 7.0 596 10607 3387 2636 4295
SpirodelaCyc 2.0 496 3638 2722 2045 3402
SwitchgrassCyc 4.0 587 14006 3379 2581 3885
TomatoCyc 2.0 588 6503 3288 2550 3880
WheatACyc 2.0 551 6315 3093 2395 3642
WheatDCyc 2.0 540 6552 3059 2335 3621

PMN Release 10.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 10.0 1214 152416 6200 5138 10960
AraCyc 13.0 620 5995 3635 2802 5242
BarleyCyc 3.0 541 5126 3033 2255 3392
BrachypodiumCyc 3.0 532 5845 3092 2289 3321
CassavaCyc 5.0 568 6957 3276 2391 3560
ChineseCabbageCyc 3.0 534 8564 3238 2337 3275
ChlamyCyc 5.0 374 3235 2597 1755 2963
CornCyc 6.0 546 7391 3296 2526 4000
GrapeCyc 5.0 558 6321 3270 2426 3527
MossCyc 4.0 474 5533 2896 2038 2883
OryzaCyc 3.0 544 6721 3373 2488 3647
PapayaCyc 4.0 539 4817 3200 2335 3304
PoplarCyc 8.0 600 8735 3395 2514 3691
PotatoCyc 2.0 559 6281 3211 2416 3456
SelaginellaCyc 4.0 482 5355 2899 2109 3007
SetariaCyc 3.0 550 6578 3114 2287 3389
SorghumBicolorCyc 3.0 541 6463 3105 2279 3420
SoyCyc 6.0 597 11619 3536 2636 4045
SpirodelaCyc 1.0 497 4052 2810 2048 3119
SwitchgrassCyc 3.0 588 15295 3471 2586 3641
TomatoCyc 1.0 589 7106 3379 2557 3634
WheatACyc 1.0 552 6868 3183 2400 3389
WheatDCyc 1.0 541 7152 3151 2349 3375

PMN Release 9.0 Update
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 9.5 1119 189957 5475 4539 9476
PapayaCyc 3.5 483 5717 2999 2143 3124

PMN Release 9.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 9.0 1119 189957 5475 4539 9476
AraCyc 12.0 634 10064 3646 2661 5054
BarleyCyc 2.0 472 7573 2955 2109 3012
BrachypodiumCyc 2.0 475 8804 2950 2108 2108
CassavaCyc 4.0 494 10010 3074 2205 3167
ChineseCabbageCyc 2.0 497 10980 3103 2218 3149
ChlamyCyc 4.0 380 3368 2442 1614 2898
CornCyc 5.0 536 14737 3088 2304 3710
GrapeCyc 4.0 485 7576 3043 2189 3170
MossCyc 3.0 428 7806 2791 1929 2764
OryzaCyc 2.0 521 11208 3103 2222 3258
PapayaCyc 3.0 483 5717 2999 2143 3124
PoplarCyc 7.0 505 20824 3124 2247 3238
SelaginellaCyc 3.0 435 6464 2802 1991 2852
SetariaCyc 2.0 481 10216 2977 2129 3061
SorghumBicolorCyc 2.0 482 9993 2986 2122 3077
SoyCyc 5.0 556 24119 3199 2263 3623
SwitchgrassCyc 2.0 494 24705 3093 2204 3158

PMN Release 8.0 Update
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 8.0 1050 188798 5332 4410 7634
AraCyc 11.5 597 9041 3490 2613 4798
BarleyCyc 1.0 465 7572 2901 2135 2880
BrachypodiumCyc 1.0 473 8802 2915 2128 2884
CassavaCyc 3.0 491 10007 3058 2232 2986
ChineseCabbageCyc 1.0 499 10976 3104 2270 2968
ChlamyCyc 3.5 349 3330 2263 1514 2708
CornCyc 4.0 508 14818 2958 2271 3436
GrapeCyc 3.0 479 7572 3015 2229 2909
MossCyc 2.0 416 7805 2713 1901 2507
OryzaCyc 1.0 482 15677 3000 2226 2987
PapayaCyc 2.0 481 5714 2999 2220 2873
PoplarCyc 6.0 505 20822 3124 2295 3115
SelaginellaCyc 2.0 421 6462 2737 1987 2630
SetariaCyc 1.0 477 10214 2942 2145 2888
SorghumBicolorCyc 1.0 480 8630 2939 2141 2928
SoyCyc 4.0 520 20317 3105 2273 3316
SwitchgrassCyc 1.0 479 17319 2985 2184 2767

PMN Release 8.0 Complete
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 8.0 1050 188798 5332 4410 7634
AraCyc 11.5 597 9041 3490 2613 4798
BarleyCyc 1.0 465 7572 2901 2135 2880
BrachypodiumCyc 1.0 473 8802 2915 2128 2884
CassavaCyc 3.0 491 10007 3058 2232 2986
ChineseCabbageCyc 1.0 499 10976 3104 2270 2968
ChlamyCyc 3.5 349 3330 2263 1514 2708
CornCyc 3.5 484 13979 2821 2160 3364
GrapeCyc 3.0 479 7572 3015 2229 2909
MossCyc 2.0 416 7805 2713 1901 2507
OryzaCyc 1.0 482 15677 3000 2226 2987
SwitchgrassCyc 1.0 479 17319 2985 2184 2767
PapayaCyc 2.0 481 5714 2999 2220 2873
PoplarCyc 6.0 505 20822 3124 2295 3115
SelaginellaCyc 2.0 421 6462 2737 1987 2630
SetariaCyc 1.0 477 10214 2942 2145 2888
SorghumBicolorCyc 1.0 480 8630 2939 2141 2928
SoyCyc 4.0 520 20317 3105 2273 3316

PMN Release 8.0 Initial
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 7.0 978 34663 3617 3455 7634
AraCyc 11.0 597 9993 3490 2613 4798
BarleyCyc 1.0 465 7572 2901 2135 2880
BrachypodiumCyc 1.0 473 8802 2915 2128 2884
CassavaCyc 3.0 491 10007 3058 2232 2986
ChlamyCyc 3.0 349 5163 2263 1514 2708
CornCyc 3.0 484 15410 2821 2160 3364
GrapeCyc 3.0 479 7572 3015 2229 2909
MossCyc 2.0 416 7805 2713 1901 2507
OryzaCyc 1.0 482 15677 3000 2226 2987
PapayaCyc 2.0 481 5714 2999 2220 2873
PoplarCyc 6.0 505 20822 3124 2295 3115
SelaginellaCyc 2.0 421 6462 2737 1987 2630
SetariaCyc 1.0 477 10214 2942 2145 2888
SorghumBicolorCyc 1.0 480 8630 2939 2141 2928
SoyCyc 4.0 520 20317 3105 2273 3316
SwitchgrassCyc 1.0 479 17319 2985 2184 2767

PMN Release 7.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 7.0 978 34663 3617 3455 7634
AraCyc 10.0 540 7127 3418 3323 4225
CassavaCyc 2.0 351 7178 2137 1538 1905
ChlamyCyc 2.0 283 2157 1688 1130 2036
CornCyc 2.0 373 10527 2198 1752 2344
GrapeCyc 2.0 359 5341 2143 1571 2037
MossCyc 1.0 335 5664 2018 1409 1869
PapayaCyc 1.0 370 3898 2165 1557 2036
PoplarCyc 5.0 381 8691 2256 1613 2099
SelaginellaCyc 1.0 329 3958 1986 1403 1838
SoyCyc 3.0 441 13055 2566 2007 2762

PMN Release 6.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 6.0 898 27652 3421 3334 6939
AraCyc 9.0 502 7100 3320 3320 3210
CassavaCyc 1.0 323 7178 2103 1815 1815
CornCyc 1.0 341 10519 2156 1731 2240
PoplarCyc 4.0 354 8691 2220 1596 2013
SoyCyc 2.0 412 13094 2528 1987 2673
GrapeCyc 1.0 330 5338 2101 1540 1933

PMN Release 5.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 5.0 810 11217 3167 3146 5734
AraCyc 8.0 446 5520 2689 2825 3346
PoplarCyc 3.0 343 3422 1906 1406 1371

PMN Release 4.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 4.0 762 11058 2929 2966 5204
AraCyc 7.0 423 5506 2418 2719 2907
PoplarCyc 2.0 323 3420 1707 1397 1092

PMN Release 3.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 3.0 714 10964 2709 2679 4803
AraCyc 6.0 408 5501 2323 2630 2691
PoplarCyc 1.0 321 3434 1668 1363 903

PMN Release 2.0
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 2.0 581 8558 2501 2464 4971
AraCyc 5.0 332 5869 1928 2312 2543

PMN Release 1.0 Inaugural
Database Pathways Enzymes Reactions Compounds Citations
PlantCyc 1.0 508 3389 2277 2314 4208
AraCyc 4.5 288 6214 1723 1956 2279

The PMN is funded by the National Science Foundation (Grant #: 1546838, 1026003 and 0640769) and the Department of Energy (BER Grant #:  ER65472 ), governed by an Editorial Board composed of internationally renowned scientists, and executed at the Carnegie Institution for Science, Department of Plant Biology.