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feat(xml-jats): parse XML JATS documents (#967)

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* chore(xml-jats): separate authors and affiliations

In XML PubMed (JATS) backend, convert authors and affiliations as they
are typically rendered on PDFs.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* fix(xml-jats): replace new line character by a space

Instead of removing new line character from text, replace it by a space character.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* feat(xml-jats): improve existing parser and extend features

Partially support lists, respect reading order, parse more sections, support equations, better text formatting.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* chore(xml-jats): rename PubMed objects to JATS

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

---------

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Cesar Berrospi Ramis
2025-02-17 10:43:31 +01:00
committed by GitHub
parent e1436a8b05
commit 428b656793
35 changed files with 13688 additions and 30671 deletions
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tests/data/groundtruth/docling_v2/bmj_sample.xml.itxt Normal file
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item-0 at level 0: unspecified: group _root_
item-1 at level 1: title: Evolving general practice consul ... Britain: issues of length and context
item-2 at level 2: paragraph: George K Freeman, John P Horder, ... on P Hill, Nayan C Shah, Andrew Wilson
item-3 at level 2: paragraph: Centre for Primary Care and Soci ... ersity of Leicester, Leicester LE5 4PW
item-4 at level 2: text: In 1999 Shah1 and others said th ... per consultation in general practice?
item-5 at level 2: text: We report on the outcome of exte ... review identified 14 relevant papers.
item-6 at level 2: section_header: Summary points
item-7 at level 3: list: group list
item-8 at level 4: list_item: Longer consultations are associa ... ith a range of better patient outcomes
item-9 at level 4: list_item: Modern consultations in general ... th more serious and chronic conditions
item-10 at level 4: list_item: Increasing patient participation ... interaction, which demands extra time
item-11 at level 4: list_item: Difficulties with access and wit ... e and lead to further pressure on time
item-12 at level 4: list_item: Longer consultations should be a ... t to maximise interpersonal continuity
item-13 at level 4: list_item: Research on implementation is needed
item-14 at level 2: section_header: Longer consultations: benefits for patients
item-15 at level 3: text: The systematic review consistent ... ther some doctors insist on more time.
item-16 at level 3: text: A national survey in 1998 report ... s the effects of their own experience.
item-17 at level 2: section_header: Context of modern consultations
item-18 at level 3: text: Shorter consultations were more ... potential length of the consultation.
item-19 at level 2: section_header: Participatory consultation style
item-20 at level 3: text: The most effective consultations ... style usually lengthens consultations.
item-21 at level 2: section_header: Extended professional agenda
item-22 at level 3: text: The traditional consultation in ... agerial expectations of good practice.
item-23 at level 3: text: Adequate time is essential. It m ... inevitably leads to pressure on time.
item-24 at level 2: section_header: Access problems
item-25 at level 3: text: In a service free at the point o ... ort notice squeeze consultation times.
item-26 at level 3: text: While appointment systems can an ... for the inadequate access to doctors.
item-27 at level 3: text: In response to perception of del ... ntation is currently being negotiated.
item-28 at level 3: text: Virtually all patients think tha ... e that is free at the point of access.
item-29 at level 3: text: A further government initiative ... ealth advice and first line treatment.
item-30 at level 2: section_header: Loss of interpersonal continuity
item-31 at level 3: text: If a patient has to consult seve ... unning and professional frustration.18
item-32 at level 3: text: Mechanic described how loss of l ... patient and professional satisfaction.
item-33 at level 2: section_header: Health service reforms
item-34 at level 3: text: Finally, for the past 15 years t ... ents and staff) and what is delivered.
item-35 at level 2: section_header: The future
item-36 at level 3: text: We think that the way ahead must ... p further the care of chronic disease.
item-37 at level 3: text: The challenge posed to general p ... ermedicalisation need to be exploited.
item-38 at level 3: text: We must ensure better communicat ... between planned and ad hoc consulting.
item-39 at level 2: section_header: Next steps
item-40 at level 3: text: General practitioners do not beh ... ailable time in complex consultations.
item-41 at level 3: text: Devising appropriate incentives ... and interpersonal knowledge and trust.
item-42 at level 2: section_header: Acknowledgments
item-43 at level 3: text: We thank the other members of th ... Practitioners for administrative help.
item-44 at level 2: section_header: References
item-45 at level 3: list: group list
item-46 at level 4: list_item: Shah NC. Viewpoint: Consultation ... y men!”. Br J Gen Pract 49:497 (1999).
item-47 at level 4: list_item: Mechanic D. How should hamsters ... BMJ 323:266–268 (2001). PMID: 11485957
item-48 at level 4: list_item: Howie JGR, Porter AMD, Heaney DJ ... n Pract 41:48–54 (1991). PMID: 2031735
item-49 at level 4: list_item: Howie JGR, Heaney DJ, Maxwell M, ... BMJ 319:738–743 (1999). PMID: 10487999
item-50 at level 4: list_item: Kaplan SH, Greenfield S, Ware JE ... c disease. Med Care 27:110–125 (1989).
item-51 at level 4: list_item: Airey C, Erens B. National surve ... e, 1998. London: NHS Executive (1999).
item-52 at level 4: list_item: Hart JT. Expectations of health ... h Expect 1:3–13 (1998). PMID: 11281857
item-53 at level 4: list_item: Tuckett D, Boulton M, Olson C, W ... London: Tavistock Publications (1985).
item-54 at level 4: list_item: General Medical Council. Draft r ... ctors/index.htm (accessed 2 Jan 2002).
item-55 at level 4: list_item: Balint M. The doctor, his patien ... the illness. London: Tavistock (1957).
item-56 at level 4: list_item: Stott NCH, Davies RH. The except ... J R Coll Gen Pract 29:210–205 (1979).
item-57 at level 4: list_item: Hill AP, Hill AP. Challenges for ... nium. London: King's Fund75–86 (2000).
item-58 at level 4: list_item: National service framework for c ... . London: Department of Health (2000).
item-59 at level 4: list_item: Hart JT. A new kind of doctor: t ... ommunity. London: Merlin Press (1988).
item-60 at level 4: list_item: Morrison I, Smith R. Hamster hea ... J 321:1541–1542 (2000). PMID: 11124164
item-61 at level 4: list_item: Arber S, Sawyer L. Do appointmen ... BMJ 284:478–480 (1982). PMID: 6800503
item-62 at level 4: list_item: Hjortdahl P, Borchgrevink CF. Co ... MJ 303:1181–1184 (1991). PMID: 1747619
item-63 at level 4: list_item: Howie JGR, Hopton JL, Heaney DJ, ... Pract 42:181–185 (1992). PMID: 1389427
item-64 at level 4: list_item: Freeman G, Shepperd S, Robinson ... ), Summer 2000. London: NCCSDO (2001).
item-65 at level 4: list_item: Wilson A, McDonald P, Hayes L, C ... Pract 41:184–187 (1991). PMID: 1878267
item-66 at level 4: list_item: De Maeseneer J, Hjortdahl P, Sta ... J 320:1616–1617 (2000). PMID: 10856043
item-67 at level 4: list_item: Freeman G, Hjortdahl P. What fut ... MJ 314:1870–1873 (1997). PMID: 9224130
item-68 at level 4: list_item: Kibbe DC, Bentz E, McLaughlin CP ... Pract 36:304–308 (1993). PMID: 8454977
item-69 at level 4: list_item: Williams M, Neal RD. Time for a ... ct 48:1783–1786 (1998). PMID: 10198490