Notes on annotation formats, mostly for biomedical literature. Examples include BioC, PubAnnotation, PubTator.
Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene.
Position can be a combination of first character in the string (zero-based index) and length, e.g. offset 72, length 20, or begin 72 and end 92.
7 8 9
0123456789012345678901234567
| |
e phosphodiesterase 8B gene.
| |
72 begin 92 end
| |
phosphodiesterase 8B
In a begin-end span, end is the position of the character immediately after the substring, in this case position 92 which is a space “ “). Subtracting end - begin gives us the length of the substring (“phosphodiesterase 8B”), in this case 20.
Below shows three different formats for PMID:20085714 (taken from https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/Format.html).
20085714|t|Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene.
20085714|a|Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.
20085714|t|Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene.
20085714|a|Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene. Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.
20085714 72 92 phosphodiesterase 8B Gene 8622
20085714 99 139 Autosomal-dominant striatal degeneration Disease 609161
20085714 671 678 c.94G>C Mutation c|SUB|G|94|C
20085714 679 687 c.95delT Mutation c|DEL|95|T
20085714 696 716 phosphodiesterase 8B Gene 8622
20085714 981 989 Dopamine Chemical D004298
...
{
"text":"Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene. Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.",
"sourcedb": "PubMed",
"sourceid": "20085714"
}
Tool-specific output format 1 (JSON, refer to PubAnnotation):
{
"text":"Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene. Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.",
"sourcedb": "PubMed",
"sourceid": "20085714",
"denotations":[
{"obj":"Gene:8622","span":{"begin":72,"end":92}},
{"obj":"Disease:609161","span":{"begin":99,"end":139}},
{"obj":"Mutation:c|SUB|G|94|C","span":{"begin":671,"end":678}},
{"obj":"Mutation:c|DEL|95|T","span":{"begin":679,"end":687}},
{"obj":"Gene:8622","span":{"begin":696,"end":716}},
{"obj":"Chemical:D004298","span":{"begin":981,"end":989}}
]
}
<collection>
<source>Example</source>
<date>1999-Jan-1</date>
<key>PubTator.key</key>
<document>
<id>20085714</id>
<passage>
<infon key="type">title</infon>
<offset>0</offset>
<text>
Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene.
</text>
</passage>
<passage>
<infon key="type">abstract</infon>
<offset>98</offset>
<text>
Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.
</text>
</passage>
</document>
</collection>
<collection>
<source>Example</source>
<date>1999-Jan-1</date>
<key>PubTator.key</key>
<document>
<id>20085714</id>
<passage>
<infon key="type">title</infon>
<offset>0</offset>
<text>
Autosomal-dominant striatal degeneration is caused by a mutation in the phosphodiesterase 8B gene.
</text>
<annotation>
<infon key="type">Gene</infon>
<offset>72</offset>
<length>20</length>
<text>phosphodiesterase 8B</text>
<id>8622</id>
</annotation>
</passage>
<passage>
<infon key="type">abstract</infon>
<offset>98</offset>
<text>
Autosomal-dominant striatal degeneration (ADSD) is an autosomal-dominant movement disorder affecting the striatal part of the basal ganglia. ADSD is characterized by bradykinesia, dysarthria, and muscle rigidity. These symptoms resemble idiopathic Parkinson disease, but tremor is not present. Using genetic linkage analysis, we have mapped the causative genetic defect to a 3.25 megabase candidate region on chromosome 5q13.3-q14.1. A maximum LOD score of 4.1 (Theta = 0) was obtained at marker D5S1962. Here we show that ADSD is caused by a complex frameshift mutation (c.94G>C+c.95delT) in the phosphodiesterase 8B (PDE8B) gene, which results in a loss of enzymatic phosphodiesterase activity. We found that PDE8B is highly expressed in the brain, especially in the putamen, which is affected by ADSD. PDE8B degrades cyclic AMP, a second messenger implied in dopamine signaling. Dopamine is one of the main neurotransmitters involved in movement control and is deficient in Parkinson disease. We believe that the functional analysis of PDE8B will help to further elucidate the pathomechanism of ADSD as well as contribute to a better understanding of movement disorders.
</text>
<annotation>
<infon key="type">Disease</infon>
<offset>99</offset>
<length>41</length>
<text>Autosomal-dominant striatal degeneration</text>
<id>609161</id>
</annotation>
<annotation>
<infon key="type">Disease</infon>
<offset>141</offset>
<length>4</length>
<text>ADSD</text>
<id>609161</id>
</annotation>
...
</passage>
</document>
</collection>
PubTator for example PMC6982432
To get annotations in JSON use the REST API, e.g. https://www.ncbi.nlm.nih.gov/research/pubtator-api/publications/export/biocjson?pmcids=PMC6982432
Donald C. Comeau, Rezarta Islamaj Doğan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur, BioC: a minimalist approach to interoperability for biomedical text processing, Database, Volume 2013, 2013, bat064, https://doi.org/10.1093/database/bat064
See also https://github.com/bionlplab/bioc