awk транспонирует выбранные строки в столбцы

$ cat tst.awk
BEGIN { OFS="\t| " }
{
    tag = val = $0
    sub(/:.*$/,"",tag)
    sub(/^[^:]+: *"?/,"",val)
    gsub(/".*$/,"",val)
    f[tag] = val
}
tag == "is_a" { print f["name"], f["def"] }

$ awk -f tst.awk file
Autosomal dominant inheritance  | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
Autosomal recessive inheritance | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).

Приведенное выше можно легко расширить для печати других значений в том же табличном формате:

$ cat tst.awk
BEGIN { OFS="\t| " }
{
    tag = val = $0
    sub(/:.*$/,"",tag)
    sub(/^[^:]+: *"?/,"",val)
    gsub(/".*$/,"",val)
    f[tag] = val
}
tag == "is_a" { print f["name"], f["id"], f["is_a"], f["def"] }

$ awk -f tst.awk file
Autosomal dominant inheritance  | HP:0000006    | HP:0000005 ! Mode of inheritance  | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
Autosomal recessive inheritance | HP:0000007    | HP:0000005 ! Mode of inheritance  | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).

Awk решение:

awk 'BEGIN{ 
         printf "%-35s | definition\n","name" 
     }
     /^name:/{ sub(/^name: /, ""); name = $0 }
     /^def:/{ 
         gsub(/^def: "|"[^"]+$/, "");
         printf "%-35s | %s\n", name, $0 
     }' file

Выход:

name                                | definition
Autosomal dominant inheritance      | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
Autosomal recessive inheritance     | A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).