The Gene Ontology Resource: 20 years and still GOing strong
(193)
Carbon, S
a
Douglass, E
a
Dunn, N
a
Good, B
a
Harris, N L
a
Lewis, S E
a
Mungall, C J
a
Basu, S
b
Chisholm, R L
b
Dodson, R J
b
Hartline, E
b
Fey, P
b
Thomas, P D
c
Albou, L P
c
Ebert, D
c
Kesling, M J
c
Mi, H
c
Muruganujan, A
c
Huang, X
c
Poudel, S
c
Mushayahama, T
c
Hu, J C
d
LaBonte, S A
d
Siegele, D A
d
Antonazzo, G
e
Attrill, H
e
Brown, N H
e
Fexova, S
e
Garapati, P
e
Jones, T E M
e
Marygold, S J
e
Millburn, G H
e
Rey, A J
e
Trovisco, V
e
Dos Santos, G
f
Emmert, D B
f
Falls, K
f
Zhou, P
f
Goodman, J L
g
Strelets, V B
g
Thurmond, J
g
Courtot, M
h
Osumi, D S
h
Parkinson, H
h
Roncaglia, P
h
Acencio, M L
i
Kuiper, M
i
Lreid, A
i
Logie, C
j
Lovering, R C
k
Huntley, R P
k
Denny, P
k
Campbell, N H
k
Kramarz, B
k
Acquaah, V
k
Ahmad, S H
k
Chen, H
k
Rawson, J H
k
Chibucos, M C
l
Giglio, M
l
Nadendla, S
l
Tauber, R
l
Duesbury, M J
h
Del, N T
h
Meldal, B H M
h
Perfetto, L
h
Porras, P
h
Orchard, S
h
Shrivastava, A
h
Xie, Z
h
Chang, H Y
h
Finn, R D
h
Mitchell, A L
h
Rawlings, N D
h
Richardson, L
h
Sangrador Vegas, A
h
Blake, J A
m
Christie, K R
m
Dolan, M E
m
Drabkin, H J
m
Hill, D P
m
Ni, L
m
Sitnikov, D
m
Harris, M A
e
Oliver, S G
e
Rutherford, K
e
Wood, V
e
Hayles, J
n
Bahler, J
k
Lock, A
k
Bolton, E R
o
De Pons, J
o
Dwinell, M
o
Hayman, G T
o
Laulederkind, S J F
o
Shimoyama, M
o
Tutaj, M
o
Wang, S J
o
D'Eustachio, P
p
Matthews, L
p
Balhoff, J P
q
Aleksander, S A
r
Binkley, G
r
Dunn, B L
r
Cherry, J M
r
Engel, S R
r
Gondwe, F
r
Karra, K
r
MacPherson, K A
r
Miyasato, S R
r
Nash, R S
r
Ng, P C
r
Sheppard, T K
r
Shrivatsav Vp, A
r
Simison, M
r
Skrzypek, M S
r
Weng, S
r
Wong, E D
r
Feuermann, M
s
Gaudet, P
s
Bakker, E
t
Berardini, T Z
t
Reiser, L
t
Subramaniam, S
t
Huala, E
t
Arighi, C
h,u,v
Auchincloss, A
h,u,v
Axelsen, K
h,u,v
Argoud, G P
h,u,v
Bateman, A
h,u,v
Bely, B
h,u,v
Blatter, M C
h,u,v
Boutet, E
h,u,v
Breuza, L
h,u,v
Bridge, A
h,u,v
Britto, R
h,u,v
Bye A Jee, H
h,u,v
Casals Casas, C
h,u,v
Coudert, E
h,u,v
Estreicher, A
h,u,v
Famiglietti, L
h,u,v
Garmiri, P
h,u,v
Georghiou, G
h,u,v
Gos, A
h,u,v
Gruaz Gumowski, N
h,u,v
Hatton Ellis, E
h,u,v
Hinz, U
h,u,v
Hulo, C
h,u,v
Ignatchenko, A
h,u,v
Jungo, F
h,u,v
Keller, G
h,u,v
Laiho, K
h,u,v
Lemercier, P
h,u,v
Lieberherr, D
h,u,v
Lussi, Y
h,u,v
Mac Dougall, A
h,u,v
Magrane, M
h,u,v
Martin, M J
h,u,v
Masson, P
h,u,v
Natale, D A
h,u,v
Hyka, N N
h,u,v
Pedruzzi, I
h,u,v
Pichler, K
h,u,v
Poux, S
h,u,v
Rivoire, C
h,u,v
Rodriguez Lopez, M
h,u,v
Sawford, T
h,u,v
Speretta, E
h,u,v
Shypitsyna, A
h,u,v
Stutz, A
h,u,v
Sundaram, S
h,u,v
Tognolli, M
h,u,v
Tyagi, N
h,u,v
Warner, K
h,u,v
Zaru, R
h,u,v
Wu, C
h,u,v
Chan, J
h,w,x,y,z
Cho, J
h,w,x,y,z
Gao, S
h,w,x,y,z
Grove, C
h,w,x,y,z
Harrison, M C
h,w,x,y,z
Howe, K
h,w,x,y,z
Lee, R
h,w,x,y,z
Mendel, J
h,w,x,y,z
Muller, H M
h,w,x,y,z
Raciti, D
h,w,x,y,z
Van Auken, K
h,w,x,y,z
Berriman, M
h,w,x,y,z
Stein, L
h,w,x,y,z
Sternberg, P W
h,w,x,y,z
Howe, D
z
Toro, S
z
Westerfield, M
z
more..
|
-
1
-
-
85016166168
-
Expansion of the Gene Ontology knowledgebase and resources
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res., 45, D331-D338.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D331-D338
-
-
-
2
-
-
84987680729
-
Standardized description of scientific evidence using the Evidence Ontology (ECO
-
bau075
-
Chibucos, M.C., Mungall, C.J., Balakrishnan, R., Christie, K.R., Huntley, R.P., White, O., Blake, J.A., Lewis, S.E. and Giglio, M. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database J. Biol. Databases Curation, 2014, bau075.
-
(2014)
Database J. Biol. Databases Curation 2014
-
-
Chibucos, M.C.1
Mungall, C.J.2
Balakrishnan, R.3
Christie, K.R.4
Huntley, R.P.5
White, O.6
Blake, J.A.7
Lewis, S.E.8
Giglio, M.9
-
3
-
-
84994493506
-
Primer on the gene ontology
-
Gaudet, P., Skunca, N., Hu, J.C. and Dessimoz, C. (2017) Primer on the gene ontology. Methods Mol. Biol., 1446, 25-37.
-
(2017)
Methods Mol. Biol
, vol.1446
, pp. 25-37
-
-
Gaudet, P.1
Skunca, N.2
Hu, J.C.3
Dessimoz, C.4
-
4
-
-
0028053411
-
Purified human MSH2 protein binds to DNA containing mismatched nucleotides
-
Fishel, R., Ewel, A. and Lescoe, M.K. (1994) Purified human MSH2 protein binds to DNA containing mismatched nucleotides. Cancer Res., 54, 5539-5542.
-
(1994)
Cancer Res
, vol.54
, pp. 5539-5542
-
-
Fishel, R.1
Ewel, A.2
Lescoe, M.K.3
-
5
-
-
84861123691
-
Ten years of pathway analysis: Current approaches and outstanding challenges
-
Khatri, P., Sirota, M. and Butte, A.J. (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol., 8, e1002375.
-
(2012)
PLoS Comput. Biol
, vol.8
, pp. e1002375
-
-
Khatri, P.1
Sirota, M.2
Butte, A.J.3
-
6
-
-
85050069830
-
Best practice data life cycle approaches for the life sciences [version 2; Referees: 2 approved]
-
Griffin, P.C., Khadake, J., LeMay, K.S., Lewis, S.E., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T. et al. (2017) Best practice data life cycle approaches for the life sciences [version 2; referees: 2 approved]. F1000Research, 6, 1618.
-
(2017)
F1000Research
, vol.6
, pp. 1618
-
-
Griffin, P.C.1
Khadake, J.2
Lemay, K.S.3
Lewis, S.E.4
Orchard, S.5
Pask, A.6
Pope, B.7
Roessner, U.8
Russell, K.9
Seemann, T.10
-
7
-
-
85045573366
-
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations
-
Christie, K.R. and Blake, J.A. (2018) Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. Cilia, 7, 3.
-
(2018)
Cilia
, vol.7
, pp. 3
-
-
Christie, K.R.1
Blake, J.A.2
-
8
-
-
85034110224
-
The Gene Ontology of eukaryotic cilia and flagella
-
Roncaglia, P., van Dam, T.J.P., Christie, K.R., Nacheva, L., Toedt, G., Huynen, M.A., Huntley, R.P., Gibson, T.J. and Lomax, J. (2017) The Gene Ontology of eukaryotic cilia and flagella. Cilia, 6, 10.
-
(2017)
Cilia
, vol.6
, pp. 10
-
-
Roncaglia, P.1
Van Dam, T.J.P.2
Christie, K.R.3
Nacheva, L.4
Toedt, G.5
Huynen, M.A.6
Huntley, R.P.7
Gibson, T.J.8
Lomax, J.9
-
9
-
-
85042224828
-
Exploring autophagy with Gene Ontology
-
Denny, P., Feuermann, M., Hill, D.P., Lovering, R.C., Plun-Favreau, H. and Roncaglia, P. (2018) Exploring autophagy with Gene Ontology. Autophagy, 14, 419-436.
-
(2018)
Autophagy
, vol.14
, pp. 419-436
-
-
Denny, P.1
Feuermann, M.2
Hill, D.P.3
Lovering, R.C.4
Plun-Favreau, H.5
Roncaglia, P.6
-
10
-
-
85045532132
-
Improving interpretation of cardiac phenotypes and enhancing discovery with expanded knowledge in the Gene Ontology
-
Lovering, R.C., Roncaglia, P., Howe, D.G., Laulederkind, S.J.F., Khodiyar, V.K., Berardini, T.Z., Tweedie, S., Foulger, R.E., Osumi-Sutherland, D., Campbell, N.H. et al. (2018) Improving interpretation of cardiac phenotypes and enhancing discovery with expanded knowledge in the Gene Ontology. Circ. Genomic Precis. Med., 11, e001813.
-
(2018)
Circ. Genomic Precis. Med
, vol.11
, pp. e001813
-
-
Lovering, R.C.1
Roncaglia, P.2
Howe, D.G.3
Laulederkind, S.J.F.4
Khodiyar, V.K.5
Berardini, T.Z.6
Tweedie, S.7
Foulger, R.E.8
Osumi-Sutherland, D.9
Campbell, N.H.10
-
11
-
-
85016120238
-
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: Case study of the apoptosis and autophagy cellular processes
-
2016, baw155
-
Feuermann, M., Gaudet, P., Mi, H., Lewis, S.E. and Thomas, P.D. (2016) Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. Database J. Biol. Databases Curation, 2016, baw155.
-
(2016)
Database J. Biol. Databases Curation
-
-
Feuermann, M.1
Gaudet, P.2
Mi, H.3
Lewis, S.E.4
Thomas, P.D.5
-
12
-
-
84992422090
-
The Protege Project: A look back and a look forward
-
Protege Team
-
Musen, M.A. and Protege Team. (2015) The Protege Project: A look back and a look forward. AI Matters, 1, 4-12.
-
(2015)
AI Matters
, vol.1
, pp. 4-12
-
-
Musen, M.A.1
-
13
-
-
0036907158
-
Extension and integration of the gene ontology (GO): Combining GO vocabularies with external vocabularies
-
Hill, D.P., Blake, J.A., Richardson, J.E. and Ringwald, M. (2002) Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res., 12, 1982-1991.
-
(2002)
Genome Res
, vol.12
, pp. 1982-1991
-
-
Hill, D.P.1
Blake, J.A.2
Richardson, J.E.3
Ringwald, M.4
-
14
-
-
84856316836
-
Uberon, an integrative multi-species anatomy ontology
-
Mungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E. and Haendel, M.A. (2012) Uberon, an integrative multi-species anatomy ontology. Genome Biol., 13, R5.
-
(2012)
Genome Biol
, vol.13
, pp. R5
-
-
Mungall, C.J.1
Torniai, C.2
Gkoutos, G.V.3
Lewis, S.E.4
Haendel, M.A.5
-
15
-
-
85016146298
-
Protein Ontology (PRO): Enhancing and scaling up the representation of protein entities
-
Natale, D.A., Arighi, C.N., Blake, J.A., Bona, J., Chen, C., Chen, S.C., Christie, K.R., Cowart, J., DEustachio, P., Diehl, A.D. et al. (2017) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res., 45, D339-D346.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D339-D346
-
-
Natale, D.A.1
Arighi, C.N.2
Blake, J.A.3
Bona, J.4
Chen, C.5
Chen, S.C.6
Christie, K.R.7
Cowart, J.8
Deustachio, P.9
Diehl, A.D.10
-
16
-
-
84874265271
-
The plant ontology as a tool for comparative plant anatomy and genomic analyses
-
Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B., Preece, J., Athreya, B., Mungall, C., Rensing, S. et al. (2013) The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol., 54, e1.
-
(2013)
Plant Cell Physiol
, vol.54
, pp. e1
-
-
Cooper, L.1
Walls, R.L.2
Elser, J.3
Gandolfo, M.A.4
Stevenson, D.W.5
Smith, B.6
Preece, J.7
Athreya, B.8
Mungall, C.9
Rensing, S.10
-
17
-
-
84976888261
-
ChEBI in 2016: Improved services and an expanding collection of metabolites
-
Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P. and Steinbeck, C. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res., 44, D1214-D1219.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. D1214-D1219
-
-
Hastings, J.1
Owen, G.2
Dekker, A.3
Ennis, M.4
Kale, N.5
Muthukrishnan, V.6
Turner, S.7
Swainston, N.8
Mendes, P.9
Steinbeck, C.10
-
18
-
-
22044433259
-
Relations in biomedical ontologies
-
Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L. and Rosse, C. (2005) Relations in biomedical ontologies. Genome Biol., 6, R46.
-
(2005)
Genome Biol
, vol.6
, pp. R46
-
-
Smith, B.1
Ceusters, W.2
Klagges, B.3
Kohler, J.4
Kumar, A.5
Lomax, J.6
Mungall, C.7
Neuhaus, F.8
Rector, A.L.9
Rosse, C.10
-
19
-
-
84856562355
-
The NCBI Taxonomy database
-
Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136-D143.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D136-D143
-
-
Federhen, S.1
-
20
-
-
79952015982
-
Evolution of the sequence ontology terms and relationships
-
Mungall, C.J., Batchelor, C. and Eilbeck, K. (2011) Evolution of the sequence ontology terms and relationships. J. Biomed. Inform., 44, 87-93.
-
(2011)
J. Biomed. Inform
, vol.44
, pp. 87-93
-
-
Mungall, C.J.1
Batchelor, C.2
Eilbeck, K.3
-
21
-
-
85040929878
-
The reactome pathway knowledgebase
-
Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Korninger, F., May, B. et al. (2018) The reactome pathway knowledgebase. Nucleic Acids Res., 46, D649-D655.
-
(2018)
Nucleic Acids Res
, vol.46
, pp. D649-D655
-
-
Fabregat, A.1
Jupe, S.2
Matthews, L.3
Sidiropoulos, K.4
Gillespie, M.5
Garapati, P.6
Haw, R.7
Jassal, B.8
Korninger, F.9
May, B.10
-
22
-
-
85019085668
-
Updates in Rhea-An expert curated resource of biochemical reactions
-
Morgat, A., Lombardot, T., Axelsen, K.B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S. et al. (2017) Updates in Rhea-An expert curated resource of biochemical reactions. Nucleic Acids Res., 45, 4279.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. 4279
-
-
Morgat, A.1
Lombardot, T.2
Axelsen, K.B.3
Aimo, L.4
Niknejad, A.5
Hyka-Nouspikel, N.6
Coudert, E.7
Pozzato, M.8
Pagni, M.9
Moretti, S.10
-
23
-
-
85058482763
-
Complex Portal 2018: Extended content and enhanced visualization tools for macromolecular complexes
-
Meldal, B.H.M., Bye-A-Jee, H., Gajdos, L., Hammerova, Z., Horackova, A., Melicher, F., Perfetto, L., Pokorny, D., Rodriguez Lopez, M., Turkova, A. et al. (2019) Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res., doi:10.1093/nar/gky1001.
-
(2019)
Nucleic Acids Res
-
-
Meldal, B.H.M.1
Bye-A-Jee, H.2
Gajdos, L.3
Hammerova, Z.4
Horackova, A.5
Melicher, F.6
Perfetto, L.7
Pokorny, D.8
Rodriguez Lopez, M.9
Turkova, A.10
-
24
-
-
85040943791
-
The MetaCyc database of metabolic pathways and enzymes
-
Caspi, R., Billington, R., Fulcher, C.A., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Midford, P.E., Ong, Q., Ong, W.K. et al. (2018) The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res., 46, D633-D639.
-
(2018)
Nucleic Acids Res
, vol.46
, pp. D633-D639
-
-
Caspi, R.1
Billington, R.2
Fulcher, C.A.3
Keseler, I.M.4
Kothari, A.5
Krummenacker, M.6
Latendresse, M.7
Midford, P.E.8
Ong, Q.9
Ong, W.K.10
-
25
-
-
84994521849
-
The gene ontology and the meaning of biological function
-
Thomas, P.D. (2017) The gene ontology and the meaning of biological function. Methods Mol. Biol., 1446, 15-24.
-
(2017)
Methods Mol. Biol
, vol.1446
, pp. 15-24
-
-
Thomas, P.D.1
-
26
-
-
84859699831
-
The Gene Ontology: Enhancements for 2011
-
Gene Ontology Consortium
-
Gene Ontology Consortium. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res., 40, D559-D564.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D559-D564
-
-
-
27
-
-
84891821006
-
Gene Ontology annotation of sequence-specific DNA binding transcription factors: Setting the stage for a large-scale curation effort
-
2013, bat062
-
Tripathi, S., Christie, K.R., Balakrishnan, R., Huntley, R., Hill, D.P., Thommesen, L., Blake, J.A., Kuiper, M. and Lreid, A. (2013) Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database J. Biol. Databases Curation, 2013, bat062.
-
(2013)
Database J. Biol. Databases Curation
-
-
Tripathi, S.1
Christie, K.R.2
Balakrishnan, R.3
Huntley, R.4
Hill, D.P.5
Thommesen, L.6
Blake, J.A.7
Kuiper, M.8
Lreid, A.9
-
28
-
-
85040950396
-
Mouse Genome Database (MGD)-2018: Knowledgebase for the laboratory mouse
-
and Mouse Genome Database Group
-
Smith, C.L., Blake, J.A., Kadin, J.A., Richardson, J.E., Bult, C.J. and Mouse Genome Database Group (2018) Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. Nucleic Acids Res., 46, D836-D842.
-
(2018)
Nucleic Acids Res
, vol.46
, pp. D836-D842
-
-
Smith, C.L.1
Blake, J.A.2
Kadin, J.A.3
Richardson, J.E.4
Bult, C.J.5
-
29
-
-
84994519272
-
The Evidence and Conclusion Ontology (ECO): Supporting GO annotations
-
Chibucos, M.C., Siegele, D.A., Hu, J.C. and Giglio, M. (2017) The Evidence and Conclusion Ontology (ECO): Supporting GO annotations. Methods Mol. Biol., 1446, 245-259.
-
(2017)
Methods Mol. Biol
, vol.1446
, pp. 245-259
-
-
Chibucos, M.C.1
Siegele, D.A.2
Hu, J.C.3
Giglio, M.4
|