(Edit 21.09.2023: I updated this for UD 2.12. The original version was for UD 2.11, but the idea is the same.)

The LINDAT/CLARIAH-CZ repository is so friendly as to allow you to automatically generate a BibTeX entry for, e.g., Universal Dependencies 2.12. But as soon as you try to use it in a LaTeX document, encoding-related warnings start popping up, and some characters might be silently rendered as tofu blocks. This comes down to a couple of issues:

  1. The Vietnamese characters ơ (\ohorn) and ư (\uhorn) are part of font encoding T5, but not T1. The Icelandic character ð (\dh) is in T1, but not in T5.

    Solution: load fontenc with the encodings T5 and T1 (in that order): \usepackage[T5,T1]{fontenc}, add \DeclareTextSymbolDefault{\ohorn}{T5} and \DeclareTextSymbolDefault{\uhorn}{T5} to the preamble, and replace the characters with {\ohorn} and {\uhorn}.

  2. The Yorùbá character ọ̀ is encoded with a diacritic glyph not recognized by T1 or T5.

    Solution: replace {\d o}̀ with {\d{\` o}}.

  3. The Icelandic character Þ/þ is represented as {\t H}/{\t h} and thus rendered as H/h with a tie bar: H͡ / h͡.

    Solution: replace {\t H} with {\TH}, and {\t h} with {\th}.

  4. There might be issues with the Romanian character ș, which can be fixed by replacing the character with \textcommabelow{s}. Likewise with Turkish ğ and {\u g}.

Here is thus the reformatted BibTeX entry for UD 2.12, to be used with

\usepackage[T5,T1]{fontenc}
\DeclareTextSymbolDefault{\ohorn}{T5}
\DeclareTextSymbolDefault{\uhorn}{T5}
@misc{zeman2023ud-2-12,
 title = {{U}niversal {D}ependencies~2.12},
 author = {Zeman, Daniel and Nivre, Joakim and 
 Abrams, Mitchell and Ackermann, Elia and Aepli, No{\"e}mi and Aghaei, Hamid and Agi{\'c}, {\v Z}eljko and Ahmadi, Amir and Ahrenberg, Lars and Ajede, Chika Kennedy and Akkurt,
 Salih Furkan and Aleksandravi{\v c}i{\=u}t{\.e}, Gabriel{\.e} and Alfina, Ika and Algom, Avner and Alnajjar, Khalid and Alzetta, Chiara and Andersen, Erik and Antonsen, Lene and Aoyama, Tatsuya and Aplonova, Katya and Aquino, Angelina and Aragon, Carolina and Aranes, Glyd and Aranzabe, Maria Jesus and Ar{\i}can, Bilge Nas and Arnard{\'o}ttir, {\TH}{\'o}runn and Arutie, Gashaw and Arwidarasti, Jessica Naraiswari and Asahara, Masayuki and {\'A}sgeirsd{\'o}ttir, Katla and Aslan, Deniz Baran and Asmazo{\u g}lu, Cengiz and Ateyah, Luma and Atmaca, Furkan and Attia, Mohammed and Atutxa, Aitziber and Augustinus, Liesbeth and Avel{\~a}s, Mariana and 
 Badmaeva, Elena and Balasubramani, Keerthana and Ballesteros, Miguel and Banerjee, Esha and Bank, Sebastian and Barbu Mititelu, Verginica and Barkarson, Starkaður and Basile, Rodolfo and Basmov, Victoria and Batchelor, Colin and Bauer, John and Bedir, Seyyit Talha and Behzad, Shabnam and Bengoetxea, Kepa and Benli, İbrahim and Ben Moshe, Yifat and Berk, G{\"o}zde and Bhat, Riyaz Ahmad and Biagetti, Erica and Bick, Eckhard and Bielinskien{\.e}, Agn{\.e} and Bjarnad{\'o}ttir, Krist{\'{\i}}n and Blokland, Rogier and Bobicev, Victoria and Boizou, Lo{\"{\i}}c and Borges V{\"o}lker, Emanuel and B{\"o}rstell, Carl and Bosco, Cristina and Bouma, Gosse and Bowman, Sam and Boyd, Adriane and Braggaar, Anouck and Branco, Ant{\'o}nio and Brokait{\.e}, Kristina and Burchardt, Aljoscha and 
 Campos, Marisa and Candito, Marie and Caron, Bernard and Caron, Gauthier and Carvalheiro, Catarina and Carvalho, Rita and Cassidy, Lauren and Castro, Maria Clara and Castro, S{\'e}rgio and Cavalcanti, Tatiana and Cebiro{\u g}lu Eryi{\u g}it, G{\"u}l{\c s}en and Cecchini, Flavio Massimiliano and Celano, Giuseppe G. A. and {\v C}{\'e}pl{\"o}, Slavom{\'{\i}}r and Cesur, Neslihan and Cetin, Savas and {\c C}etino{\u g}lu, {\"O}zlem and Chalub, Fabricio and Chamila, Liyanage and Chauhan, Shweta and Chi, Ethan and Chika, Taishi and Cho, Yongseok and Choi, Jinho and Chun, Jayeol and Chung, Juyeon and Cignarella, Alessandra T. and Cinkov{\'a}, Silvie and Collomb, Aur{\'e}lie and {\c C}{\"o}ltekin, {\c C}a{\u g}r{\i} and Connor, Miriam and Corbetta, Daniela and Costa, Francisco and Courtin, Marine and Cristescu, Mihaela and 
 Dale, Ingerid L{\o}yning and Daniel, Philemon and Davidson, Elizabeth and de Alencar, Leonel Figueiredo and Dehouck, Mathieu and de Laurentiis, Martina and de Marneffe, Marie-Catherine and de Paiva, Valeria and Derin, Mehmet Oguz and de Souza, Elvis and Diaz de Ilarraza, Arantza and Dickerson, Carly and Dinakaramani, Arawinda and Di Nuovo, Elisa and Dione, Bamba and Dirix, Peter and Dobrovoljc, Kaja and Doyle, Adrian and Dozat, Timothy and Droganova, Kira and Dwivedi, Puneet and 
 Ebert, Christian and Eckhoff, Hanne and Eguchi, Masaki and Eiche, Sandra and Eli, Marhaba and Elkahky, Ali and Ephrem, Binyam and Erina, Olga and Erjavec, Toma{\v z} and Essaidi, Farah and Etienne, Aline and Evelyn, Wograine and 
 Facundes, Sidney and Farkas, Rich{\'a}rd and Favero, Federica and Ferdaousi, Jannatul and Fernanda, Mar{\'{\i}}lia and Fernandez Alcalde, Hector and Fethi, Amal and Foster, Jennifer and Freitas, Cl{\'a}udia and Fujita, Kazunori and 
 Gajdo{\v s}ov{\'a}, Katar{\'{\i}}na and Galbraith, Daniel and Gamba, Federica and Garcia, Marcos and G{\"a}rdenfors, Moa and Gerardi, Fabr{\'{\i}}cio Ferraz and Gerdes, Kim and Gessler, Luke and Ginter, Filip and Godoy, Gustavo and Goenaga, Iakes and Gojenola, Koldo and G{\"o}k{\i}rmak, Memduh and Goldberg, Yoav and G{\'o}mez Guinovart, Xavier and Gonz{\'a}lez Saavedra,
 Berta and Grici{\=u}t{\.e}, Bernadeta and Grioni, Matias and Grobol, Lo{\"{\i}}c and Gr{\= u}z{\={\i}}tis, Normunds and Guillaume, Bruno and Guillot-Barbance, C{\'e}line and G{\"u}ng{\"o}r, Tunga and 
 Habash, Nizar and Hafsteinsson, Hinrik and Haji{\v c}, Jan and Haji{\v c} jr., Jan and H{\"a}m{\"a}l{\"a}inen, Mika and H{\`a} M{\~y}, Linh and Han, Na-Rae and Hanifmuti, Muhammad Yudistira and Harada, Takahiro and Hardwick, Sam and Harris, Kim and Haug, Dag and Heinecke, Johannes and Hellwig, Oliver and Hennig, Felix and Hladk{\'a}, Barbora and Hlav{\'a}{\v c}ov{\'a}, Jaroslava and Hociung, Florinel and Hohle, Petter and Huerta Mendez, Marivel and Hwang, Jena and 
 Ikeda, Takumi and Ingason, Anton Karl and Ion, Radu and Irimia, Elena and Ishola, {\d O}l{\'a}j{\'{\i}}d{\'e} and Islamaj, Artan and Ito, Kaoru and 
 Jannat, Siratun and Jel{\'{\i}}nek, Tom{\'a}{\v s} and Jha, Apoorva and Jiang, Katharine and Johannsen, Anders and J{\'o}nsd{\'o}ttir, Hildur and J{\o}rgensen, Fredrik and Juutinen, Markus and 
 Ka{\c s}{\i}kara, H{\"u}ner and Kabaeva, Nadezhda and Kahane, Sylvain and Kanayama, Hiroshi and Kanerva, Jenna and Kara, Neslihan and Karah{\'o}{\u g}a, Ritv{\'a}n and K{\aa}sen, Andre and Kayadelen, Tolga and Kengatharaiyer, Sarveswaran and Kettnerov{\'a}, V{\'a}clava and Kirchner, Jesse and Klementieva, Elena and Klyachko, Elena and K{\"o}hn, Arne and K{\"o}ksal, Abdullatif and Kopacewicz, Kamil and Korkiakangas, Timo and K{\"o}se, Mehmet and Koshevoy, Alexey and Kotsyba, Natalia and Kovalevskait{\.e}, Jolanta and Krek, Simon and Krishnamurthy, Parameswari and K{\"u}bler, Sandra and Kuqi, Adrian and Kuyruk{\c c}u, O{\u g}uzhan and Kuzgun, Asl{\i} and Kwak, Sookyoung and Kyle, Kris and 
 Laippala, Veronika and Lambertino, Lorenzo and Lando, Tatiana and Larasati, Septina Dian and Lavrentiev, Alexei and Lee, John and L{\^e} H{\`{\^o}}ng, Ph{\uhorn}{\ohorn}ng and Lenci, Alessandro and Lertpradit, Saran and Leung, Herman and Levina, Maria and Levine, Lauren and Li, Cheuk Ying and Li, Josie and Li, Keying and Li, Yixuan and Li, Yuan and Lim, {KyungTae} and Lima Padovani, Bruna and Lin, Yi-Ju Jessica and Lind{\'e}n, Krister and Liu, Yang Janet and Ljube{\v s}i{\'c}, Nikola and Loginova, Olga and Lusito, Stefano and Luthfi, Andry and Luukko, Mikko and Lyashevskaya, Olga and Lynn, Teresa and 
 Macketanz, Vivien and Mahamdi, Menel and Maillard, Jean and Makarchuk, Ilya and Makazhanov, Aibek and Mandl, Michael and Manning, Christopher and Manurung, Ruli and Mar{\c s}an, B{\"u}{\c s}ra and M{\u a}r{\u a}nduc, C{\u a}t{\u a}lina and Mare{\v c}ek, David and Marheinecke, Katrin and Markantonatou, Stella and Mart{\'{\i}}nez Alonso, H{\'e}ctor and Mart{\'{\i}}n Rodr{\'{\i}}guez, Lorena and Martins, Andr{\'e} and Martins, Cl{\'a}udia and Ma{\v s}ek, Jan and Matsuda, Hiroshi and Matsumoto, Yuji and Mazzei, Alessandro and {McDonald}, Ryan and {McGuinness}, Sarah and Mendon{\c c}a, Gustavo and Merzhevich, Tatiana and Miekka, Niko and Miller, Aaron and Mischenkova, Karina and Missil{\"a}, Anna and Mititelu, C{\u a}t{\u a}lin and Mitrofan, Maria and Miyao, Yusuke and Mojiri Foroushani, {AmirHossein} and Moln{\'a}r, Judit and Moloodi, Amirsaeid and Montemagni, Simonetta and More, Amir and Moreno Romero, Laura and Moretti, Giovanni and Mori, Shinsuke and Morioka, Tomohiko and Moro, Shigeki and Mortensen, Bjartur and Moskalevskyi, Bohdan and Muischnek, Kadri and Munro, Robert and Murawaki, Yugo and M{\"u}{\"u}risep, Kaili and 
 Nainwani, Pinkey and Nakhl{\'e}, Mariam and Navarro Hor{\~n}iacek, Juan Ignacio and Nedoluzhko,
 Anna and Ne{\v s}pore-B{\=e}rzkalne, Gunta and Nevaci, Manuela and Nguy{\~{\^e}}n Th{\d i}, L{\uhorn}{\ohorn}ng and Nguy{\~{\^e}}n Th{\d i} Minh, Huy{\`{\^e}}n and Nikaido, Yoshihiro and Nikolaev, Vitaly and Nitisaroj, Rattima and Nourian, Alireza and Nurmi, Hanna and 
 Ojala, Stina and Ojha, Atul Kr. and {\'O}lad{\'o}ttir, Hulda and Ol{\'u}{\`o}kun, Ad{\'e}day{\d{\` o}} and Omura, Mai and Onwuegbuzia, Emeka and Ordan, Noam and Osenova, Petya and {\"O}stling, Robert and {\O}vrelid, Lilja and {\"O}zate{\c s}, {\c S}aziye Bet{\"u}l and {\"O}z{\c c}elik, Merve and {\"O}zg{\"u}r, Arzucan and {\"O}zt{\"u}rk Ba{\c s}aran, Balk{\i}z and 
 Paccosi, Teresa and Palmero Aprosio, Alessio and Panova, Anastasia and Park, Hyunji Hayley and Partanen, Niko and Pascual, Elena and Passarotti, Marco and Patejuk, Agnieszka and Paulino-Passos, Guilherme and Pedonese, Giulia and Peljak-{\L}api{\'n}ska, Angelika and Peng, Siyao and Peng, Siyao Logan and Pereira, Rita and Pereira, S{\'{\i}}lvia and Perez, Cenel-Augusto and Perkova, Natalia and Perrier, Guy and Petrov, Slav and Petrova, Daria and Peverelli, Andrea and Phelan, Jason and Piitulainen, Jussi and Pinter, Yuval and Pinto, Clara and Pirinen, Tommi A and Pitler, Emily and Plamada, Magdalena and Plank, Barbara and Poibeau, Thierry and Ponomareva, Larisa and Popel, Martin and Pretkalni{\c n}a, Lauma and Pr{\'e}vost, Sophie and Prokopidis, Prokopis and Przepi{\'o}rkowski, Adam and Pugh, Robert and Puolakainen, Tiina and Pyysalo, Sampo and 
 Qi, Peng and Querido, Andreia and 
 R{\"a}{\"a}bis, Andriela and Rademaker, Alexandre and Rahoman, Mizanur and Rama, Taraka and Ramasamy, Loganathan and Ramos, Joana and Rashel, Fam and Rasooli, Mohammad Sadegh and Ravishankar, Vinit and Real, Livy and Rebeja, Petru and Reddy, Siva and Regnault, Mathilde and Rehm, Georg and Riabi, Arij and Riabov, Ivan and Rie{\ss}ler, Michael and Rimkut{\.e}, Erika and Rinaldi, Larissa and Rituma, Laura and Rizqiyah, Putri and Rocha, Luisa and R{\"o}gnvaldsson, Eir{\'{\i}}kur and Roksandic, Ivan and Romanenko, Mykhailo and Rosa, Rudolf and Ro\textcommabelow{s}ca, Valentin and Rovati, Davide and Rozonoyer, Ben and Rudina, Olga and Rueter, Jack and R{\'u}narsson, Kristj{\'a}n and 
 Sadde, Shoval and Safari, Pegah and Sahala, Aleksi and Saleh, Shadi and Salomoni, Alessio and Samard{\v z}i{\'c}, Tanja and Samson, Stephanie and Sanguinetti, Manuela and San{\i}yar, Ezgi and S{\"a}rg, Dage and Sartor, Marta and Sasaki,  Mitsuya and Saul{\={\i}}te, Baiba and Sawanakunanon, Yanin and Saxena, Shefali and Scannell, Kevin and Scarlata, Salvatore and Schneider, Nathan and Schuster, Sebastian and Schwartz, Lane and Seddah, Djam{\'e} and Seeker, Wolfgang and Seraji, Mojgan and Shahzadi, Syeda and Shen, Mo and Shimada, Atsuko and Shirasu, Hiroyuki and Shishkina, Yana and Shohibussirri, Muh and Shvedova, Maria and Siewert, Janine and Sigurðsson, Einar Freyr and Silva, Jo{\~a}o and Silveira, Aline and Silveira, Natalia and Silveira, Sara and Simi, Maria and Simionescu, Radu and Simk{\'o}, Katalin and {\v S}imkov{\'a}, M{\'a}ria and S{\'{\i}}monarson, Haukur Barri and Simov, Kiril and Sitchinava, Dmitri and Sither, Ted and Skachedubova, Maria and Smith, Aaron and Soares-Bastos, Isabela and Solberg, Per Erik and Sonnenhauser, Barbara and Sourov, Shafi and Sprugnoli, Rachele and Stamou, Vivian and Steingr{\'{\i}}msson, Stein{\th}{\'o}r and Stella, Antonio and Stephen, Abishek and Straka, Milan and Strickland, Emmett and Strnadov{\'a}, Jana and Suhr, Alane and Sulestio, Yogi Lesmana and Sulubacak, Umut and Suzuki, Shingo and Swanson, Daniel and Sz{\'a}nt{\'o}, Zsolt and 
 Taguchi, Chihiro and Taji, Dima and Tamburini, Fabio and Tan, Mary Ann C. and Tanaka, Takaaki and Tanaya, Dipta and Tavoni, Mirko and Tella, Samson and Tellier, Isabelle and Testori, Marinella and Thomas, Guillaume and Tonelli, Sara and Torga, Liisi and Toska, Marsida and Trosterud, Trond and Trukhina, Anna and Tsarfaty, Reut and T{\"u}rk, Utku and Tyers, Francis and {\TH}{\'o}rðarson, Sveinbj{\"o}rn and {\TH}orsteinsson, Vilhj{\'a}lmur and 
 Uematsu, Sumire and Untilov, Roman and Ure{\v s}ov{\'a}, Zde{\v n}ka and Uria, Larraitz and Uszkoreit, Hans and Utka, Andrius and 
 Vagnoni, Elena and Vajjala, Sowmya and Vak, Socrates and van der Goot, Rob and Vanhove, Martine and van Niekerk, Daniel and van Noord, Gertjan and Varga, Viktor and Vedenina, Uliana and Venturi, Giulia and Vincze, Veronika and Vlasova, Natalia and 
 Wakasa, Aya and Wallenberg, Joel C. and Wallin, Lars and Walsh, Abigail and Washington, Jonathan North and Wendt, Maximilan and Widmer, Paul and Wigderson, Shira and Wijono, Sri Hartati and Williams, Seyi and Wir{\'e}n, Mats and Wittern, Christian and Woldemariam, Tsegay and Wong, Tak-sum and Wr{\'o}blewska, Alina and 
 Yako, Mary and Yamashita, Kayo and Yamazaki, Naoki and Yan, Chunxiao and Yasuoka, Koichi and Yavrumyan, Marat M. and Yenice, Arife Bet{\"u}l and Y{\i}ld{\i}z, Olcay Taner and Yu, Zhuoran and Yuliawati, Arlisa and 
 {\v Z}abokrtsk{\'y}, Zden{\v e}k and Zahra, Shorouq and Zeldes, Amir and Zhou, He and Zhu, Hanzhi and Zhu, Yilun and Zhuravleva, Anna and Ziane, Rayan},
 url = {http://hdl.handle.net/11234/1-5150},
 note = {{LINDAT}/{CLARIAH}-{CZ} digital library at the Institute of Formal and Applied Linguistics ({{\'U}FAL}), Faculty of Mathematics and Physics, Charles University},
 copyright = {Licence Universal Dependencies v2.12},
 year = {2023}
}

(Is the resulting bibliography entry too long? That’s for whoever created your BibTeX style file to decide. The relevant setting is nmlm.)