Some sample data demonstrating https://github.com/svjan5/medtype/issues/14

commands.sh

# Commands used to generate the other two files
head -n 70 medmentions.json | tail -n 1 > medmentions-line-70.json
head -n 2 pubmed_ds/split_0.txt | tail -n 1 > pubmed-line-2.json

medmentions-line-70.json

{
  "_id": "27245524",
  "title": "Ehlers-Danlos syndrome",
  "abstract": "The Ehlers-Danlos syndromes (EDSs) were originally described by Ehlers in Denmark and Danlos in Paris in 1898 and 1908, respectively. They had both published individual case studies in which the common factor was laxity of ligaments leading to joint hypermobility and hyperextensibility of the skin. The choice of the name of this eponymous disease had been made by Dr Parkes Weber, an eminent London physician in the 1930s, who had a penchant for eponymous diseases, having had no less than seven attributed to himself, at least in part. Unfortunately, this was before the age of a computerised literature search, and Parkes Weber had inadvertently overlooked the very first description of EDS which had been made by Tchernabogov, a Russian dermatologist, whose description was published in 1891 and remains one of the best descriptions of EDS in the literature.",
  "text": "Ehlers-Danlos syndrome The Ehlers-Danlos syndromes (EDSs) were originally described by Ehlers in Denmark and Danlos in Paris in 1898 and 1908, respectively. They had both published individual case studies in which the common factor was laxity of ligaments leading to joint hypermobility and hyperextensibility of the skin. The choice of the name of this eponymous disease had been made by Dr Parkes Weber, an eminent London physician in the 1930s, who had a penchant for eponymous diseases, having had no less than seven attributed to himself, at least in part. Unfortunately, this was before the age of a computerised literature search, and Parkes Weber had inadvertently overlooked the very first description of EDS which had been made by Tchernabogov, a Russian dermatologist, whose description was published in 1891 and remains one of the best descriptions of EDS in the literature.",
  "mentions": [
    {
      "start_offset": 0,
      "end_offset": 22,
      "mention": "Ehlers-Danlos syndrome",
      "category": "T047",
      "link_id": "C0013720"
    },
    {
      "start_offset": 27,
      "end_offset": 50,
      "mention": "Ehlers-Danlos syndromes",
      "category": "T047",
      "link_id": "C0013720"
    },
    {
      "start_offset": 52,
      "end_offset": 56,
      "mention": "EDSs",
      "category": "T047",
      "link_id": "C0013720"
    },
    {
      "start_offset": 74,
      "end_offset": 83,
      "mention": "described",
      "category": "T170",
      "link_id": "C0678257"
    },
    {
      "start_offset": 87,
      "end_offset": 93,
      "mention": "Ehlers",
      "category": "T016",
      "link_id": "C0086418"
    },
    {
      "start_offset": 97,
      "end_offset": 104,
      "mention": "Denmark",
      "category": "T083",
      "link_id": "C0011318"
    },
    {
      "start_offset": 109,
      "end_offset": 115,
      "mention": "Danlos",
      "category": "T016",
      "link_id": "C0086418"
    },
    {
      "start_offset": 119,
      "end_offset": 124,
      "mention": "Paris",
      "category": "T083",
      "link_id": "C0030561"
    },
    {
      "start_offset": 171,
      "end_offset": 180,
      "mention": "published",
      "category": "T057",
      "link_id": "C0034037"
    },
    {
      "start_offset": 192,
      "end_offset": 204,
      "mention": "case studies",
      "category": "T170",
      "link_id": "C0085973"
    },
    {
      "start_offset": 236,
      "end_offset": 255,
      "mention": "laxity of ligaments",
      "category": "T046",
      "link_id": "C0158359"
    },
    {
      "start_offset": 267,
      "end_offset": 286,
      "mention": "joint hypermobility",
      "category": "T184",
      "link_id": "C0086437"
    },
    {
      "start_offset": 291,
      "end_offset": 321,
      "mention": "hyperextensibility of the skin",
      "category": "T033",
      "link_id": "C0241074"
    },
    {
      "start_offset": 341,
      "end_offset": 345,
      "mention": "name",
      "category": "T170",
      "link_id": "C0027365"
    },
    {
      "start_offset": 354,
      "end_offset": 371,
      "mention": "eponymous disease",
      "category": "T170",
      "link_id": "C0282574"
    },
    {
      "start_offset": 389,
      "end_offset": 404,
      "mention": "Dr Parkes Weber",
      "category": "T016",
      "link_id": "C0086418"
    },
    {
      "start_offset": 417,
      "end_offset": 423,
      "mention": "London",
      "category": "T083",
      "link_id": "C0023973"
    },
    {
      "start_offset": 424,
      "end_offset": 433,
      "mention": "physician",
      "category": "T097",
      "link_id": "C0031831"
    },
    {
      "start_offset": 458,
      "end_offset": 466,
      "mention": "penchant",
      "category": "T055",
      "link_id": "C3826173"
    },
    {
      "start_offset": 471,
      "end_offset": 489,
      "mention": "eponymous diseases",
      "category": "T170",
      "link_id": "C0282574"
    },
    {
      "start_offset": 606,
      "end_offset": 629,
      "mention": "computerised literature",
      "category": "T170",
      "link_id": "C0023866"
    },
    {
      "start_offset": 630,
      "end_offset": 636,
      "mention": "search",
      "category": "T052",
      "link_id": "C1706202"
    },
    {
      "start_offset": 642,
      "end_offset": 654,
      "mention": "Parkes Weber",
      "category": "T016",
      "link_id": "C0086418"
    },
    {
      "start_offset": 699,
      "end_offset": 710,
      "mention": "description",
      "category": "T170",
      "link_id": "C0678257"
    },
    {
      "start_offset": 714,
      "end_offset": 717,
      "mention": "EDS",
      "category": "T047",
      "link_id": "C0013720"
    },
    {
      "start_offset": 741,
      "end_offset": 753,
      "mention": "Tchernabogov",
      "category": "T016",
      "link_id": "C0086418"
    },
    {
      "start_offset": 757,
      "end_offset": 764,
      "mention": "Russian",
      "category": "T098",
      "link_id": "C0337816"
    },
    {
      "start_offset": 765,
      "end_offset": 778,
      "mention": "dermatologist",
      "category": "T097",
      "link_id": "C0259831"
    },
    {
      "start_offset": 786,
      "end_offset": 797,
      "mention": "description",
      "category": "T170",
      "link_id": "C0678257"
    },
    {
      "start_offset": 802,
      "end_offset": 811,
      "mention": "published",
      "category": "T057",
      "link_id": "C0034037"
    },
    {
      "start_offset": 848,
      "end_offset": 860,
      "mention": "descriptions",
      "category": "T170",
      "link_id": "C0678257"
    },
    {
      "start_offset": 864,
      "end_offset": 867,
      "mention": "EDS",
      "category": "T047",
      "link_id": "C0013720"
    },
    {
      "start_offset": 875,
      "end_offset": 885,
      "mention": "literature",
      "category": "T170",
      "link_id": "C0023866"
    }
  ],
  "split": "train"
}

pubmed-line-2.json

{
  "_id": "15971595",
  "text": "[Chemical induction -- new strategy of oocyte enucleation]. Mammalian somatic cloning has got great progress during past few years,however,the efficiency of nuclear trasfer remains low. In order to improve this technique, different perspectives of which are studying. Accordingly, the method of oocyte enucleation also becomes a focus. But the physical enucleation is technically demanding, time-consuming, inherently invasive and clearly damaging to cytoplast spatial organization. As a alternative strategy to traditional method, Demecolcine-induced enucleation(IE) attracted the scientist's eyes. Nuclear transfer procedure assited with IE, factors releated with success rate of IE and effects of IE on the oocytes and cloned embryos are mainly discussed in this review. At the same time, combining with author's research, the existing problems of IE and potential improved measures of some key steps in IE procedure are also elucidated. However, the utility of the demecolcine-induced enucleation protocol will require further deep investigation.",
  "title": "[Chemical induction -- new strategy of oocyte enucleation].",
  "mentions": [
    {
      "mention": "oocytes",
      "start_offset": 710,
      "end_offset": 717,
      "link_id": "C0029045",
      "mesh_id": "D009865"
    }
  ]
}