Release Notes

PMN Release 11.0

Released: 
June 2016
Release Information: 

The data content of all 23 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

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Overview
Overall Highlights: 

We are pleased to announce the PMN11 release. Highlights include the addition of curated information of rate-limiting steps in over 50 pathways. To see an example, follow this link,

http://pmn.plantcyc.org/PLANT/NEW-IMAGE?type=PATHWAY&object=PWY-695

To see a complete list of pathways with rate-limiting info, follow this link,

http://pmn.plantcyc.org/group?id=pmn-prod.dpb.carnegiescience.edu-1-3673...

Clicking on any pathway from the SmartTable, you will see a pathway diagram where the rate-limiting reaction is indicated with an icon of hourglass. Mouse over the icon to see the literature source of the curated rate-limiting data. We will continue curating and adding available rate-limiting data from the literature.

In this release we removed additional data of macro-molecule metabolism from the PMN databases, including enzymes, reactions and pathways that metabolize or modify proteins, DNAs, and RNAs.

The PMN databases are now updated to the Pathway Tools 19.5 data schema.

Collaborator Release Notes: 

You can find more information on the releases provided by our collaborators at MetaCyc, the multi-species, multi-kingdom database, in their Release Notes

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