Difference between revisions of "2018"
(21 intermediate revisions by the same user not shown) | |||
Line 15: | Line 15: | ||
{| border="1" cellpading="2" | {| border="1" cellpading="2" | ||
|- | |- | ||
− | ! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IEP !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! IKR !! HEP !! HMP !! HGI | + | ! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IEP !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! IKR !! HEP !! HMP !! HGI || EXP |
|- | |- | ||
! WormBase | ! WormBase | ||
− | | 8031 (454)|| 3208 (90) || 1132 (33) || 324 (1) || 105 || 108 (11) || 51 || 63 (10) || 22 || 2 || 2 || 0 || 2 || 189 || 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 | ||
− | | | + | |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 | ||
− | | | + | | 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 || | + | | 2 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 12247 || 0 || 0 || 0 || 0 || 0 |
|- | |- | ||
!ParkinsonsUK-UCL | !ParkinsonsUK-UCL | ||
− | | | + | | 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 | ||
− | | | + | | 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 |
|} | |} | ||
Line 62: | Line 68: | ||
|- | |- | ||
!IntAct | !IntAct | ||
− | | 0 || 0 || 0 || 0 || 0 || | + | | 0 || 0 || 0 || 0 || 0 || 2238 (60) || 0 || 0 || 0 || 0 || 0 || 0 || 0 |
|- | |- | ||
!UniProt | !UniProt | ||
− | | | + | | 117 (13) || 26 || 185 (9) || 231 (16) || 24 (1) || 511 (3) || 123 || 50 || 0 || 123 || 0 || 0 || 0 |
|- | |- | ||
!CACAO | !CACAO | ||
Line 71: | Line 77: | ||
|- | |- | ||
!GO_Central | !GO_Central | ||
− | | 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || | + | | 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 | ||
− | |||
− | |||
− | |||
|- | |- | ||
!Totals | !Totals | ||
− | | | + | | 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 | ||
− | | | + | | 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 || | + | | 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 10565 || 0 || 0 |
|- | |- | ||
!UniProt | !UniProt | ||
− | | | + | | 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 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 |
− | |||
− | |||
− | |||
|- | |- | ||
!SynGO | !SynGO | ||
− | | | + | | 29 || 0 ||89 (8) || 1 (1) || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 2 |
|- | |- | ||
!Totals | !Totals | ||
− | | | + | | 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 | + | Summary Statistics Based on WormBase Release WS268 |
Genes Stats: | Genes Stats: | ||
− | Genes with GO_term connections | + | Genes with GO_term connections 13883 |
− | Non-IEA-only annotation | + | Non-IEA-only annotation 1135 |
− | IEA-only annotation | + | IEA-only annotation 6293 |
− | Both IEA and non-IEA annotations | + | Both IEA and non-IEA annotations 6455 |
GO_term Stats: | GO_term Stats: | ||
− | Distinct GO_terms connected to Genes | + | Distinct GO_terms connected to Genes 6094 |
− | Associated by non-IEA only | + | Associated by non-IEA only 3482 |
− | Associated by IEA only | + | Associated by IEA only 882 |
− | Associated by both IEA and non-IEA | + | Associated by both IEA and non-IEA 1730 |
{| class="wikitable" style="text-align:center" | {| class="wikitable" style="text-align:center" | ||
Line 152: | Line 152: | ||
|- | |- | ||
| Interpro2GO | | Interpro2GO | ||
− | | | + | | 21465 |
|- | |- | ||
| Other (e.g. Swiss-Prot keyword mapping) | | Other (e.g. Swiss-Prot keyword mapping) | ||
− | | | + | | 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 |