Difference between revisions of "2018"

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(Created page with "= Annotation Progress = '''WormBase GO Annotation Statistics as of December 5, 2018''' Manual annotation statistics are summarized in Tables 1 - 3. Total number of unique m...")
 
 
(25 intermediate revisions by the same user not shown)
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Manual annotation statistics are summarized in Tables 1 - 3.
 
Manual annotation statistics are summarized in Tables 1 - 3.
  
Total number of unique manual annotations: 44384 (+3.8% from 2016)
+
Total number of unique manual annotations: 52557 (+18.4% from 2017)
  
Total number of genes with manual annotations: 7508 (-1.1% from 2016)
+
Total number of genes with manual annotations: 7850 (+4.5% from 2017)
  
 
'''Table 1: Summary of ''C. elegans'' Manual Biological Process Annotations'''
 
'''Table 1: Summary of ''C. elegans'' Manual Biological Process Annotations'''
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{| border="1" cellpading="2"
 
{| border="1" cellpading="2"
 
|-
 
|-
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IEP !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! IKR !! HMP !! HGI
+
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IEP !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! IKR !! HEP !! HMP !! HGI || EXP
 
|-
 
|-
 
! WormBase
 
! WormBase
| 8102 (451)|| 3215 (92) || 1135 (33) || 328 (1) || 108 || 310 (18) || 51 || 73 (10) || 24 || 2 || 3 || 0 || 1 || 0 || 0
+
| 8031 (454)|| 3208 (90) || 1132 (33) || 324 (1) || 105 || 108 (11) || 51 || 63 (10) || 22 || 2 || 2 || 0 || 2 || 189 || 0 || 0 || 0
 
|-
 
|-
 
!UniProt  
 
!UniProt  
|3189 (751) || 2331 (369) || 212 (22) || 203 || 29 (3) || 14 || 2 (2) || 5 || 103 || 0 || 68 || 0 || 0 || 18(18) || 135 (135)  
+
|3483 (831) || 2694 (508) || 218 (23) || 209 || 29 (3) || 23 || 2 (2) || 4 || 101 || 0 || 66  || 0 || 0 || 0 || 0 || 0 || 0
 +
|-
 +
! SynGO
 +
| 48 (37) || 69 (44) || 0 || 0 || 0 || 0 || 0 || 0|| 0 || 0 || 0  || 0 || 0 || 0 || 0 || 0 || 10
 
|-
 
|-
 
!CACAO
 
!CACAO
| 20 || 1 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 18 || 1 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0  
 
|-     
 
|-     
 
!BHF-UCL
 
!BHF-UCL
| 11 || 0 || 0 || 2 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 11 || 0 || 0 || 2 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
|-
 
|-
 
!MGI
 
!MGI
| 4 || 0 || 6 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 4 || 0 || 6 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0  
 
|-
 
|-
 
!HGNC
 
!HGNC
| 0 || 0 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 0 || 0 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
|-
 
|-
 
!GO_Central
 
!GO_Central
| 2 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 7430 || 0 || 0 || 0  
+
| 2 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 12247 || 0 || 0 || 0 || 0 || 0  
 
|-
 
|-
 
!ParkinsonsUK-UCL
 
!ParkinsonsUK-UCL
| 14 (4) || 9 (3) || 11 || 3 (1) || 0  || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 10 (4) || 6 (3) || 11 || 2 (1) || 0  || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0  
 
|-
 
|-
 
!CAFA
 
!CAFA
| 2 || 0 || 2 || 0 || 0  || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 2 || 0 || 2 || 0 || 0  || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 +
|-
 +
!SGD
 +
| 0 || 0 || 0 || 1 (1) || 0  || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0  
 
|-
 
|-
 
!Totals
 
!Totals
| 11344 (1206) || 5556 (464) || 1369 (55) || 540 (2) || 137 (3) || 328 (18) || 53 (2) || 83 (10) || 127 || 2 || 71 || 7530 || 1 || 18 (18) || 135 (135)
+
| 11609 (1326) || 5978 (645) || 1372 (55) || 542 (3) || 134 (3) || 135 (11) || 53 (2) || 67 (10) || 123 || 2 || 68 || 12247 || 2 || 189 || 0 || 0 || 0
 
|}
 
|}
  
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|-
 
|-
 
! WormBase
 
! WormBase
| 174 (11) || 32 || 1895 (214) ||  653 (5) || 45 || 1355 (5) || 22 || 4 || 3 || 79 || 0 || 2 || 2
+
| 172 (11) || 32 || 1899 (214) ||  643 (7) || 33 || 1355 (5) || 21 (1) || 4 || 3 || 80 || 0 || 2 || 3
 
|-
 
|-
 
!IntAct  
 
!IntAct  
| 0 || 0 || 0 || 0 || 0 || 2250 (56) || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 0 || 0 || 0 || 0 || 0 || 2238 (60) || 0 || 0 || 0 || 0 || 0 || 0 || 0  
 
|-
 
|-
 
!UniProt  
 
!UniProt  
| 111 (11) || 23 || 165 (5) || 198 || 24 (1) || 458 (3) || 4 || 51 || 0 || 123 || 0 || 0 || 0
+
| 117 (13) || 26 || 185 (9) || 231 (16) || 24 (1) || 511 (3) || 123 || 50 || 0 || 123 || 0 || 0 || 0
 
|-  
 
|-  
 
!CACAO
 
!CACAO
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|-
 
|-
 
!GO_Central
 
!GO_Central
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 5957 || 0 || 1
+
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 9803 || 0 || 1
 
|-
 
|-
 
!HGNC
 
!HGNC
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!CAFA
 
!CAFA
 
| 1 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
| 1 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
 
!Reactome
 
| 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
 
|-
 
|-
 
!Totals
 
!Totals
| 287 (22) || 55 || 2067 (219) || 853 (5) || 70 (1) || 4066 (66) || 26 || 55 || 3 || 202 || 5957 || 2 || 3
+
| 291 (24) || 58 || 2091 (223) || 876 (23) || 57 (1) || 4107 (70) || 144 (1) || 54 || 3 || 203 || 9803 || 2 || 4
 
|}
 
|}
  
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{| border="1" cellpading="2"
 
{| border="1" cellpading="2"
 
|-
 
|-
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IPI !! IC !! NAS !! ISM !! ND !! IBA  
+
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! HDA !! EXP
 
|-
 
|-
 
! WormBase
 
! WormBase
| 9 || 0 || 6674 (798) ||  386 || 27 || 143 (3) || 50 (1) || 7 || 4 || 12 || 0  
+
| 7 || 0 || 5622 (348) ||  379 || 27 || 140 (3) || 49 || 7 || 4 || 12 || 0 || 545 (452) || 0
 
|-
 
|-
 
!GO_Central
 
!GO_Central
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 6063
+
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 10565 || 0 || 0
 
|-
 
|-
 
!UniProt
 
!UniProt
| 72 (22) || 1 || 711 (100) ||  233 || 20 || 1 || 19 || 49 || 0 || 117 || 0  
+
| 80 (24) || 1 || 742 (104) ||  219 || 20 || 1 || 16 || 47 || 0 || 116 || 0 || 0 || 0
 
|-
 
|-
 
!MGI
 
!MGI
| 0 || 0 || 16 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 0 || 0 || 16 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
|-
 
|-
 
!HGNC
 
!HGNC
| 0 || 0 || 0 || 8 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 0 || 0 || 0 || 8 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
|-
 
|-
 
! BHF-UCL
 
! BHF-UCL
| 0 || 0 || 7 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0  
+
| 0 || 0 || 7 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
 
|-
 
|-
 
!CACAO
 
!CACAO
| 0 || 0 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
+
| 0 || 0 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
 
!Reactome
 
| 0 || 0 || 0 || 0 || 8 || 0 || 0 || 0 || 0 || 0 || 0  
 
 
|-
 
|-
 
!SynGO
 
!SynGO
| 0 || 0 || 0 || 1 (1) || 0 || 0 || 0 || 0 || 0 || 0 || 0  
+
| 29 || 0 ||89 (8) || 1 (1) || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 2
 
|-
 
|-
 
!Totals
 
!Totals
| 81 (22) || 1 || 7411 (898) || 620 (1) || 55 || 144 (3) || 69 (1) || 56 || 4 || 129 || 6063
+
| 116 || 1 || 6479 (460) || 607 (1) || 47 || 141 (3) || 65 || 54 || 4 || 128 || 10565 || 545 (452) || 2
 
|}
 
|}
  
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'''Table 4: Summary of ''C. elegans'' Computational Annotations'''
 
'''Table 4: Summary of ''C. elegans'' Computational Annotations'''
  
Summary Statistics Based on WormBase Release WS262
+
Summary Statistics Based on WormBase Release WS268
  
 
Genes Stats:
 
Genes Stats:
   Genes with GO_term connections  13880
+
   Genes with GO_term connections  13883
     Non-IEA-only annotation            1170
+
     Non-IEA-only annotation            1135
     IEA-only annotation                6290
+
     IEA-only annotation                6293
     Both IEA and non-IEA annotations    6420
+
     Both IEA and non-IEA annotations    6455
  
 
GO_term Stats:
 
GO_term Stats:
   Distinct GO_terms connected to Genes  6023
+
   Distinct GO_terms connected to Genes  6094
     Associated by non-IEA only              3567
+
     Associated by non-IEA only              3482
     Associated by IEA only                    817
+
     Associated by IEA only                    882
     Associated by both IEA and non-IEA      1639
+
     Associated by both IEA and non-IEA      1730
  
 
{| class="wikitable" style="text-align:center"
 
{| class="wikitable" style="text-align:center"
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|-
 
|-
 
| Interpro2GO  
 
| Interpro2GO  
| 21823
+
| 21465
 
|-
 
|-
 
| Other (e.g. Swiss-Prot keyword mapping)       
 
| Other (e.g. Swiss-Prot keyword mapping)       
| 44965
+
| 44502
 
|-  
 
|-  
 
|}
 
|}

Latest revision as of 13:40, 17 December 2018

Annotation Progress

WormBase GO Annotation Statistics as of December 5, 2018

Manual annotation statistics are summarized in Tables 1 - 3.

Total number of unique manual annotations: 52557 (+18.4% from 2017)

Total number of genes with manual annotations: 7850 (+4.5% from 2017)

Table 1: Summary of C. elegans Manual Biological Process Annotations

Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.

Annotation Group IMP IGI IDA ISS TAS IEP IPI IC NAS ISM ND IBA IKR HEP HMP HGI EXP
WormBase 8031 (454) 3208 (90) 1132 (33) 324 (1) 105 108 (11) 51 63 (10) 22 2 2 0 2 189 0 0 0
UniProt 3483 (831) 2694 (508) 218 (23) 209 29 (3) 23 2 (2) 4 101 0 66 0 0 0 0 0 0
SynGO 48 (37) 69 (44) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10
CACAO 18 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BHF-UCL 11 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0
MGI 4 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HGNC 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0
GO_Central 2 0 0 0 0 0 0 0 0 0 0 12247 0 0 0 0 0
ParkinsonsUK-UCL 10 (4) 6 (3) 11 2 (1) 0 0 0 0 0 0 0 0 0 0 0 0 0
CAFA 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SGD 0 0 0 1 (1) 0 0 0 0 0 0 0 0 0 0 0 0 0
Totals 11609 (1326) 5978 (645) 1372 (55) 542 (3) 134 (3) 135 (11) 53 (2) 67 (10) 123 2 68 12247 2 189 0 0 0


Table 2: Summary of C. elegans Molecular Function Annotations

Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.

Annotation Group IMP IGI IDA ISS TAS IPI IC NAS ISM ND IBA ISO IKR
WormBase 172 (11) 32 1899 (214) 643 (7) 33 1355 (5) 21 (1) 4 3 80 0 2 3
IntAct 0 0 0 0 0 2238 (60) 0 0 0 0 0 0 0
UniProt 117 (13) 26 185 (9) 231 (16) 24 (1) 511 (3) 123 50 0 123 0 0 0
CACAO 1 0 7 0 0 0 0 0 0 0 0 0 0
GO_Central 0 0 0 0 0 0 0 0 0 0 9803 0 1
HGNC 0 0 0 2 0 0 0 0 0 0 0 0 0
ParkinsonsUK-UCL 0 0 0 0 0 2 (2) 0 0 0 0 0 0 0
CAFA 1 0 0 0 0 1 0 0 0 0 0 0 0
Totals 291 (24) 58 2091 (223) 876 (23) 57 (1) 4107 (70) 144 (1) 54 3 203 9803 2 4


Table 3: Summary of C. elegans Cellular Component Annotations

Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.

Annotation Group IMP IGI IDA ISS TAS IPI IC NAS ISM ND IBA HDA EXP
WormBase 7 0 5622 (348) 379 27 140 (3) 49 7 4 12 0 545 (452) 0
GO_Central 0 0 0 0 0 0 0 0 0 0 10565 0 0
UniProt 80 (24) 1 742 (104) 219 20 1 16 47 0 116 0 0 0
MGI 0 0 16 0 0 0 0 0 0 0 0 0 0
HGNC 0 0 0 8 0 0 0 0 0 0 0 0 0
BHF-UCL 0 0 7 0 0 0 0 0 0 0 0 0 0
CACAO 0 0 3 0 0 0 0 0 0 0 0 0 0
SynGO 29 0 89 (8) 1 (1) 0 0 0 0 0 0 0 0 2
Totals 116 1 6479 (460) 607 (1) 47 141 (3) 65 54 4 128 10565 545 (452) 2


Table 4: Summary of C. elegans Computational Annotations

Summary Statistics Based on WormBase Release WS268

Genes Stats:

 Genes with GO_term connections  13883 
   Non-IEA-only annotation             1135
   IEA-only annotation                 6293
   Both IEA and non-IEA annotations    6455

GO_term Stats:

 Distinct GO_terms connected to Genes   6094
   Associated by non-IEA only               3482
   Associated by IEA only                    882
   Associated by both IEA and non-IEA       1730
Type of Annotation IEA
Interpro2GO 21465
Other (e.g. Swiss-Prot keyword mapping) 44502