From the first Bodley had fixed upon James as his library keeper, and the appointment was confirmed by the university in 1602. On 14 Sept. of that year he also became rector of St. Aldate, Oxford. His salary as librarian was at the commencement 5l. 13s. 4d. quarterly, but he threatened forthwith to resign unless it was raised to 30l. or 40l. a year. At the same time he demanded permission to marry. Bodley, who had made celibacy a stringent condition in his statutes, expostulated with James on his 'unseasonable and unreasonable motions,' but eventually allowed him to take a wife (Reliquiæ Bodleianæ, pp. 52, 163, 183). In 1605 appeared the first catalogue of the library compiled by James, and dedicated to Henry, prince of Wales, at the suggestion of Bodley, who thought that 'more reward was to be gained from the prince than from the king' (ib. p. 200). It includes both printed books and manuscripts, arranged alphabetically under the four classes of theology, medicine, law, and arts. A continuation of this classified index, embracing writers on arts and sciences, geography and history, is to be found in Rawlinson MS. Miscell. 730, drawn up by James after quitting the library for the use of young students. An alphabetical catalogue prepared by him in 1613 in 'two small hand-books ' was not printed, but remains in the library. In December 1610 the library began to receive copies of all works published by the members of the Stationers' Company, in pursuance of an agreement made with them by Bodley at the suggestion of James. In 1614 James, through Bodley's interest, was preferred to the sub-deanery of Wells.and in 1617 he became rector of Mongeham,Kent. At the beginning of May 1620 he was obliged through ill-health to resign the librarianship, but not before he had superintended the preparation of a second edition of the catalogue, which appeared in the ensuing July. It abandons the classified arrangement of the former catalogue, and adopts only one alphabet of names. There was also issued in 1635 'Catalogus Interpretum S. Scripturee juxta numerorum ordinem qui extant in Bibliotheca Bodleiana olim a D. Jamesio … concinnatus, nunc vero altera fere parte auctior redditus. … Editio correcta,' 4to, Oxford.
At the convocation held with the parliament at Oxford in 1626 he moved that certain scholars be commissioned to peruse the patristic manuscripts in all public and priyate English libraries in order to detect the forgeries introduced by Roman catholic editors. His proposal not meeting with much encouragement, he set about the task himself. James died at Oxford in August 1629, and was buried in New College Chapel. One portrait of him hangs in the Bodleian Library; another is in the library of Sion College (Hearne, Collections, Oxf. Hist. Soc., iii. 416).
James's works not already described are:
- 'Bellum Papale, sive Concordia discors Sixti Quinti & Clementis Octavi circa Hieronymianam Editionem,' 4to, London, 1600; 12mo, 1678.
- 'Concordantio sanctorum Patrum, i.e. vera & pia Libri Canticorum per Patres universos, tam Graecos quam Latinos, Expositio,' 4to, Oxford, 1607.
- 'An Apologie for John Wickliffe, shewing his Conformitie with the new Church of England,' 4to, Oxford, 1608; in answer to Robert Parsons and others.
- 'Bellum Gregorianum, sive Corruptionis Romanae in Operibus D. Gregorii M. jussu Pontificum Rom. recognitis atque editis ex Typographlca Vaticana loca insigniora, observata, Theologia ad hoc officium deputatis,' s. sh. 4to, Oxford, 1610.
- 'A Treatise of the Corruption of Scripture, Counsels, and Fathers, by … the Church of Rome. … Together with a sufficient Answere unto J. Gretser and A. Possevine, Jesuites, and the unknowne Author of the Grounds of the Old Religion and the New,' 5 pts. 4to, London, 1611; other editions in 1612, 1688, and 1843.
- 'The Jesuits Downefall threatened against them by the Secular Priests for their wicked lives, accursed manners, heretical doctrine, etc. Together with the Life of Father Parsons,' 4to, Oxford, 1612.
- 'Index generalis sanctorum Patrum, ad singulos versus cap. 5. secundum Matthaeum,' 8vo, London, 1624.
- 'G. Wicelii Methodus Concordim Ecclesiasticæ … Adjectre sunt notee … et vita ipsius … unn cum enumeratione auctorum qui scripserunt contra squalores … Curiae Romanae,' 8vo, London, 1625.
- 'Vindiciæ Gregorianæ, seu restitutus innumeris paene locis Gregorias M., ex variis manuscriptis … collatis,' 4to, Geneva, 1625, with a preface by B. Turrettinus.
- 'A Manduction or Introduction unto Divinitie: containing a confutation of Papists by Papists throughout the important Articles of our Religion,' 4to, Oxford, 1625.
- 'The humble … Request of T. James to the Church of England, for, and in the behalfe of; Bookes touching Religion,' 16mo, Oxford? 1625?
- 'An Explanation or Enlarging of the Ten Articles in the Supplication of Doctor James, lately exhibited to the Clergy of England' [in reference to a projected new edition of the 'Fathers'], 4to, Oxford, 1626.
- 'Specimen Corruptelarum Pontificiorum in Cypriano, Ambrosio, Gregorio M. et Authore operis imperfecli, & in jure canonico,' 4to, London, 1626.